Mercurial > repos > galaxyp > openms_msfraggeradapter
changeset 5:9866e1170611 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:05:24 +0000 |
| parents | e133b5c8878f |
| children | 907fda39b333 |
| files | MSFraggerAdapter.xml fill_ctd.py fill_ctd_clargs.py generate-foo.sh macros.xml macros_autotest.xml macros_test.xml readme.md test-data.sh test-data/spectrast.log |
| diffstat | 10 files changed, 414 insertions(+), 27987 deletions(-) [+] |
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--- a/MSFraggerAdapter.xml Mon Dec 14 16:55:52 2020 +0000 +++ b/MSFraggerAdapter.xml Thu Dec 01 19:05:24 2022 +0000 @@ -1,13 +1,25 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> -<tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05"> - <description>Peptide Identification with MSFragger</description> +<tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>Peptide Identification with MSFragger. +Important note: +The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute +the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available +for use on related service offerings supported by the University of Tubingen and the Center for +Integrative Bioinformatics. +Per the license agreement the use of the pipeline and associated materials is for academic +research, non-commercial or educational purposes. Any commercial use inquiries +must be directed to the University of Michigan Technology Transfer Office at +techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the +University of Michigan. + +For details, please see the supplied license file or +https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt +</description> <macros> <token name="@EXECUTABLE@">MSFraggerAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -58,48 +70,66 @@ <configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="java_heapmemory" argument="-java_heapmemory" type="integer" optional="true" value="3500" label="Maximum Java heap size (in MB)" help=""/> - <param name="in" argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/> - <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Protein FASTA database file path" help=" select fasta data sets(s)"/> + <param argument="-license" display="radio" type="select" optional="false" label="Set to yes, if you have read and agreed to the MSFragger license terms" help=""> + <option value="yes">yes</option> + <option value="no">no</option> + <expand macro="list_string_san" name="license"/> + </param> + <param argument="-java_heapmemory" type="integer" optional="true" value="3500" label="Maximum Java heap size (in MB)" help=""/> + <param argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/> + <param argument="-database" type="data" format="fasta" optional="false" label="Protein FASTA database file path" help=" select fasta data sets(s)"/> + <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/> <section name="tolerance" title="Search Tolerances" help="" expanded="false"> - <param name="precursor_mass_tolerance" argument="-tolerance:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Precursor mass tolerance (window is +/- this value)" help=""/> - <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> + <param name="precursor_mass_tolerance_lower" argument="-tolerance:precursor_mass_tolerance_lower" type="float" optional="true" min="0.0" value="20.0" label="Lower precursor mass tolerance" help=""/> + <param name="precursor_mass_tolerance_upper" argument="-tolerance:precursor_mass_tolerance_upper" type="float" optional="true" min="0.0" value="20.0" label="Upper precursor mass tolerance" help=""/> + <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="precursor_mass_unit"/> </param> <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" optional="true" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/> - <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" display="radio" type="select" optional="false" label="Unit of precursor true tolerance" help=""> + <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" optional="true" label="Unit of precursor true tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="precursor_true_unit"/> </param> <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/> - <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help=""> + <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_mass_unit"/> </param> - <param name="isotope_error" argument="-tolerance:isotope_error" display="radio" type="select" optional="false" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12"> + <param name="isotope_error" argument="-tolerance:isotope_error" type="select" optional="true" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12"> <option value="0" selected="true">0</option> <option value="1">1</option> <option value="2">2</option> - <expand macro="list_string_san"/> + <option value="0/1/2">0/1/2</option> + <expand macro="list_string_san" name="isotope_error"/> </param> </section> <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false"> - <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="false" label="Name of the enzyme to be written to the pepXML file" help=""> - <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="true" label="Name of the enzyme to be written to the pepXML file" help=""> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C">Arg-C</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Asp-N">Asp-N</option> <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> <option value="Clostripain/P">Clostripain/P</option> - <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> - <option value="no cleavage">no cleavage</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Arg-C">Arg-C</option> - <option value="Arg-C/P">Arg-C/P</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> <option value="Lys-C">Lys-C</option> <option value="Lys-N">Lys-N</option> <option value="Lys-C/P">Lys-C/P</option> @@ -107,43 +137,33 @@ <option value="TrypChymo">TrypChymo</option> <option value="Trypsin/P">Trypsin/P</option> <option value="V8-DE">V8-DE</option> - <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="Alpha-lytic protease">Alpha-lytic protease</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="iodosobenzoate">iodosobenzoate</option> - <option value="Asp-N">Asp-N</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="CNBr">CNBr</option> - <option value="Formic_acid">Formic_acid</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> <option value="Trypsin" selected="true">Trypsin</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="search_enzyme_name"/> </param> <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="search_enzyme_cutafter"/> </param> <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" optional="true" value="P" label="Residues that the enzyme will not cut before" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="search_enzyme_nocutbefore"/> </param> - <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" display="radio" type="select" optional="false" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help=""> + <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" optional="true" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help=""> <option value="non-enzymatic">non-enzymatic</option> <option value="semi">semi</option> <option value="fully" selected="true">fully</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="num_enzyme_termini"/> </param> - <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="false" label="Allowed number of missed cleavages" help=""> + <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="true" label="Allowed number of missed cleavages" help=""> <option value="0">0</option> <option value="1">1</option> <option value="2" selected="true">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="allowed_missed_cleavage"/> </param> <param name="min_length" argument="-digest:min_length" type="integer" optional="true" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/> <param name="max_length" argument="-digest:max_length" type="integer" optional="true" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/> @@ -153,22 +173,26 @@ <section name="varmod" title="Variable Modification Parameters" help="" expanded="false"> <param name="clip_nterm_m" argument="-varmod:clip_nterm_m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Specifies the trimming of a protein N-terminal methionine as a variable modification" help=""/> <param name="masses" argument="-varmod:masses" type="text" optional="true" value="" label="Masses for variable modifications" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_float_valsan"/> + <expand macro="list_float_valsan" name="masses"/> </param> <param name="syntaxes" argument="-varmod:syntaxes" type="text" optional="true" value="" label="Syntax Strings for variable modifications" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <expand macro="list_string_val" name="syntaxes"/> + <expand macro="list_string_san" name="syntaxes"/> + </param> + <param name="unimod" argument="-varmod:unimod" type="text" optional="true" value="" label="Variable modifications in unimod syntax, is added to mass+syntax varmod list" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="unimod"/> + <expand macro="list_string_san" name="unimod"/> </param> <param name="enable_common" argument="-varmod:enable_common" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable common variable modifications (15.9949 M and 42.0106 [^)" help=""/> <param name="not_allow_multiple_variable_mods_on_residue" argument="-varmod:not_allow_multiple_variable_mods_on_residue" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not allow any one amino acid to be modified by multiple variable modifications" help=""/> - <param name="max_variable_mods_per_mod" argument="-varmod:max_variable_mods_per_mod" type="select" optional="false" label="Maximum number of residues that can be occupied by each variable modification" help=""> + <param name="max_variable_mods_per_peptide" argument="-varmod:max_variable_mods_per_peptide" type="select" optional="true" label="Maximum total number of variable modifications per peptide" help=""> <option value="0">0</option> <option value="1">1</option> <option value="2" selected="true">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="max_variable_mods_per_peptide"/> </param> <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" optional="true" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/> </section> @@ -178,12 +202,12 @@ <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/> <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/> <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/> - <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" display="radio" type="select" optional="false" label="Maximum charge state for theoretical fragments to match" help=""> + <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" optional="true" label="Maximum charge state for theoretical fragments to match" help=""> <option value="1">1</option> <option value="2" selected="true">2</option> <option value="3">3</option> <option value="4">4</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="max_fragment_charge"/> </param> <param name="override_charge" argument="-spectrum:override_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)" help=""/> <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" optional="true" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/> @@ -198,6 +222,7 @@ <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" optional="true" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/> <param name="output_report_topn" argument="-search:output_report_topn" type="integer" optional="true" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/> <param name="output_max_expect" argument="-search:output_max_expect" type="float" optional="true" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/> + <param name="localize_delta_mass" argument="-search:localize_delta_mass" type="integer" optional="true" min="0" value="0" label="Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)" help=""/> </section> <section name="statmod" title="Static Modification Parameters" help="" expanded="false"> <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/> @@ -224,11 +249,89 @@ <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/> <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/> <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/> + <param name="unimod" argument="-statmod:unimod" type="text" optional="true" value="" label="Fixed modifications in unimod syntax if specific mass is unknown" help="e.g. Carbamidomethylation (C). When multiple different masses are given for one aminoacid this parameter (unimod) will have priority (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="unimod"/> + <expand macro="list_string_san" name="unimod"/> + </param> + </section> + <section name="PeptideIndexing" title="" help="" expanded="false"> + <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> + <expand macro="list_string_san" name="decoy_string"/> + </param> + <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> + <option value="prefix" selected="true">prefix</option> + <option value="suffix">suffix</option> + <expand macro="list_string_san" name="decoy_string_position"/> + </param> + <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> + <option value="error">error</option> + <option value="warn" selected="true">warn</option> + <option value="silent">silent</option> + <expand macro="list_string_san" name="missing_decoy_action"/> + </param> + <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> + <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> + <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> + <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> + <option value="error" selected="true">error</option> + <option value="warn">warn</option> + <option value="remove">remove</option> + <expand macro="list_string_san" name="unmatched_action"/> + </param> + <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/> + <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> + <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> + <section name="enzyme" title="" help="" expanded="false"> + <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> + <option value="auto" selected="true">auto</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Trypsin">Trypsin</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> + <option value="Glu-C+P">Glu-C+P</option> + <option value="PepsinA + P">PepsinA + P</option> + <option value="cyanogen-bromide">cyanogen-bromide</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Asp-N">Asp-N</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Arg-C">Arg-C</option> + <expand macro="list_string_san" name="name"/> + </param> + <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> + <option value="auto" selected="true">auto</option> + <option value="full">full</option> + <option value="semi">semi</option> + <option value="none">none</option> + <expand macro="list_string_san" name="specificity"/> + </param> + </section> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -245,13 +348,26 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MSFraggerAdapter"/> - <expand macro="manutest_MSFraggerAdapter"/> + <tests><!-- TOPP_MSFraggerAdapter_7 --> + <!-- TOPP_MSFraggerAdapter_8 --> </tests> - <help><![CDATA[Peptide Identification with MSFragger + <help><![CDATA[Peptide Identification with MSFragger. +Important note: +The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute +the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available +for use on related service offerings supported by the University of Tubingen and the Center for +Integrative Bioinformatics. +Per the license agreement the use of the pipeline and associated materials is for academic +research, non-commercial or educational purposes. Any commercial use inquiries +must be directed to the University of Michigan Technology Transfer Office at +techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the +University of Michigan. + +For details, please see the supplied license file or +https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSFraggerAdapter.html]]></help> + +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSFraggerAdapter.html]]></help> <expand macro="references"/> </tool>
--- a/fill_ctd.py Mon Dec 14 16:55:52 2020 +0000 +++ b/fill_ctd.py Thu Dec 01 19:05:24 2022 +0000 @@ -32,7 +32,7 @@ for k, v in e.items(): if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)): mergeDicts(d[k], e[k]) - elif k not in d and not isinstance(e[k], collections.abc.Mapping): + elif k not in d: d[k] = e[k] else: sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) @@ -135,9 +135,10 @@ # insert the hc_args into the args mergeDicts(args, hc_args) -if "adv_opts_cond" in args: - args.update(args["adv_opts_cond"]) - del args["adv_opts_cond"] +# put the contents of the advanced options section into the main dict +if "adv_opts" in args: + args.update(args["adv_opts"]) + del args["adv_opts"] # IDMapper has in and spectra:in params, in is used in out as format_source", # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fill_ctd_clargs.py Thu Dec 01 19:05:24 2022 +0000 @@ -0,0 +1,70 @@ +#!/usr/bin/env python3 + +import operator +from argparse import ArgumentParser +from functools import reduce # forward compatibility for Python 3 +from io import StringIO + +from CTDopts.CTDopts import ( + _Null, + CTDModel, + ModelTypeError, + Parameters +) + + +def getFromDict(dataDict, mapList): + return reduce(operator.getitem, mapList, dataDict) + + +def setInDict(dataDict, mapList, value): + getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value + + +if __name__ == "__main__": + # note add_help=False since otherwise arguments starting with -h will + # trigger an error (despite allow_abbreviate) + parser = ArgumentParser(prog="fill_ctd_clargs", + description="fill command line arguments" + "into a CTD file and write the CTD file to stdout", + add_help=False, allow_abbrev=False) + parser.add_argument("--ini_file", dest="ini_file", help="input ini file", + metavar='INI', default=None, required=True) + parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" + "if given then optional parameters from the ini file" + "will be filled with the defaults from this CTD file", + metavar='CTD', default=None, required=False) + args, cliargs = parser.parse_known_args() + + # load CTDModel + ini_model = None + try: + ini_model = CTDModel(from_file=args.ini_file) + except ModelTypeError: + pass + try: + ini_model = Parameters(from_file=args.ini_file) + except ModelTypeError: + pass + assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) + + # get a dictionary of the ctd arguments where the values of the parameters + # given on the command line are overwritten + ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) + + if args.ctd_file: + ctd_model = CTDModel(from_file=args.ctd_file) + ctd_values = ctd_model.get_defaults() + for param in ini_model.get_parameters(): + if not param.required and (param.default is None or type(param.default) is _Null): + lineage = param.get_lineage(name_only=True) + try: + default = getFromDict(ctd_values, lineage) + except KeyError: + continue + setInDict(ini_values, lineage, default) + + # write the ctd with the values taken from the dictionary + out = StringIO() + ctd_tree = ini_model.write_ctd(out, ini_values) + print(out.getvalue())
--- a/generate-foo.sh Mon Dec 14 16:55:52 2020 +0000 +++ b/generate-foo.sh Thu Dec 01 19:05:24 2022 +0000 @@ -8,17 +8,15 @@ # get the tests from the CMakeLists.txt # 1st remove some tests - # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 + # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt # - several tools with duplicated input (leads to conflict when linking) - # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) # - some input files are originally in a subdir (degenerated cases/), but not in test-data - # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) - # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002 - # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's@${DATA_DIR_SHARE}/@@g' | grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | @@ -26,19 +24,9 @@ grep -v "MaRaClusterAdapter.*-consensus_out"| grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | sed 's@degenerate_cases/@@g' | - grep -v 'TOPP_SeedListGenerator_3"' | egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | - egrep -v '"TOPP_FeatureFinderIdentification_4"' | - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/') - - -# grep -v 'FileFilter.*-spectra:select_polarity ""' | -# grep -v 'MassTraceExtractor_2.ini ' | -# grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" | -# grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" | -# grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" | -# grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" | -# grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" | + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + grep -v '"TOPP_SiriusAdapter_10"') # 1st part is a dirty hack to join lines containing a single function call, e.g. # addtest(.... @@ -50,6 +38,7 @@ # >&2 echo $line test_id=$(echo "$line" | cut -d" " -f 1) tool_id=$(echo "$line" | cut -d" " -f 2) + # >&2 echo "test_id $test_id" if [[ $test_id =~ _out_?[0-9]? ]]; then >&2 echo " skip $test_id $line" continue @@ -67,7 +56,7 @@ tes=" <test>\n" line=$(fix_tmp_files "$line") line=$(unique_files "$line") - # >&2 echo $line + # >&2 echo LINE $line #if there is an ini file then we use this to generate the test #otherwise the ctd file is used #other command line parameters are inserted later into this xml @@ -77,19 +66,23 @@ else ini="ctd/$tool_id.ctd" fi + # >&2 echo "========================================================" + # >&2 echo "USING ini $ini" cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') ctdtmp=$(mktemp) - #echo python3 fill_ctd_clargs.py --ctd $ini $cli # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) - # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" - eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" - # echo $ctdtmp + # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" + eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" + # >&2 echo $ctdtmp # >&2 cat $ctdtmp testtmp=$(mktemp) - python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null + # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" + CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null + echo "<!-- $test_id -->" cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' - rm $ctdtmp $testtmp + + rm "$ctdtmp" "$testtmp" #> /dev/null @@ -130,23 +123,23 @@ #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) #this function replaces the tmp file by the expected file. function fix_tmp_files { -# >&2 echo "FIX $line" + # >&2 echo "FIX $line" ret="" for a in $@; do - if [[ ! $a =~ .tmp$ ]]; then + # >&2 echo " a "$a + if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then ret="$ret $a" continue fi -# >&2 echo " a "$a - g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") -# >&2 echo " g "$g - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g) + diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") + # >&2 echo " diff_line "$diff_line + in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) # >&2 echo " in1 "$in1 if [[ "$a" != "$in1" ]]; then ret="$ret $a" continue fi - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g) + in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) in2=$(basename $in2 | sed 's/)$//') # >&2 echo " in2 "$in2 if [[ -f "test-data/$in2" ]]; then @@ -176,11 +169,11 @@ fi ln -f -s $in1 test-data/$in2 done - for i in test-data/*.tmp - do + + find test-data/ -name "*.tmp" -print0 | + while IFS= read -r -d '' i; do if [ ! -e test-data/$(basename $i .tmp) ]; then ln -s $(basename $i) test-data/$(basename $i .tmp) - #ln -s $(basename $i) test-data/$(basename $i .tmp) else ln -fs $(basename $i) test-data/$(basename $i .tmp) fi @@ -194,14 +187,14 @@ # id=$1 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" -# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | sed 's/degenerate_cases\///' | egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | grep add_test | egrep "TOPP|UTILS" | sed 's@${DATA_DIR_SHARE}/@@g;'| - sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'| + sed 's@${TMP_RIP_PATH}@./@g'| sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | while read line
--- a/macros.xml Mon Dec 14 16:55:52 2020 +0000 +++ b/macros.xml Thu Dec 01 19:05:24 2022 +0000 @@ -3,14 +3,15 @@ You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> - <token name="@TOOL_VERSION@">2.6</token> - <token name="@GALAXY_VERSION@">0</token> + <token name="@TOOL_VERSION@">2.8</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> - <!-- makeblastdb for OMSSAAdapter --> - <requirement type="package" version="2.9.0">blast</requirement> + <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> + <requirement type="package" version="2.1.9">omssa</requirement> + <requirement type="package" version="2.13.0">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> @@ -33,23 +34,15 @@ </citations> </xml> <xml name="adv_opts_macro"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"/> - <when value="advanced"> - <yield/> - </when> - </conditional> + <section name="adv_opts" title="Advanced Options" expanded="false"> + <yield/> + </section> </xml> <!-- sanitizers and validators --> - <xml name="list_string_val"> - <validator type="regex" message="parameter must not start with $">^[^$]</validator> - - <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> + <xml name="list_string_val" token_name=""> + <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> + <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> </xml> <xml name="list_string_san"> <sanitizer> @@ -65,8 +58,8 @@ </valid> </sanitizer> </xml> - <xml name="list_float_valsan"> - <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> + <xml name="list_float_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -79,8 +72,8 @@ </valid> </sanitizer> </xml> - <xml name="list_integer_valsan"> - <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> + <xml name="list_integer_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -120,11 +113,11 @@ </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) - #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) - #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def ]]></token></macros>
--- a/macros_autotest.xml Mon Dec 14 16:55:52 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27189 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<macros> - <xml name="autotest_AccurateMassSearch"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/> - <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AccurateMassSearch_2_input.featureXML"/> - <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> - <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AccurateMassSearch_2_input.featureXML"/> - <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> - <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_AssayGeneratorMetabo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="true"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="true"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="100.0"/> - <param name="max_fragment_mz" value="900.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_BaselineFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="BaselineFilter_input.mzML"/> - <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="struc_elem_length" value="1.5"/> - <param name="struc_elem_unit" value="Thomson"/> - <param name="method" value="tophat"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ClusterMassTracesByPrecursor"> -</xml> - <xml name="autotest_ClusterMassTraces"> -</xml> - <xml name="autotest_CometAdapter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="1000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="5"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.50025"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.25"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="1"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep any known"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="1000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="5"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CometAdapter_2_prepared.mzML"/> - <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="CometAdapter_2_in.fasta"/> - <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="Da"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.50025"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.25"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="1"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep any known"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="20000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="3"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CometAdapter_3.mzML"/> - <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="CometAdapter_3.fasta"/> - <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.01"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="3"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep known search unknown"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:1200"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="20000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="3"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/> - <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.01"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="3"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep known search unknown"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="variable_modifications" value="Met-loss (Protein N-term M)"/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CompNovoCID"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CompNovoCID_1_input.mzML"/> - <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="algorithm"> - <param name="max_number_aa_per_decomp" value="4"/> - <param name="tryptic_only" value="true"/> - <param name="precursor_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="max_number_pivot" value="9"/> - <param name="max_subscore_number" value="40"/> - <param name="decomp_weights_precision" value="0.01"/> - <param name="double_charged_iso_threshold" value="0.6"/> - <param name="max_mz" value="2000.0"/> - <param name="min_mz" value="200.0"/> - <param name="max_isotope_to_score" value="3"/> - <param name="max_decomp_weight" value="450.0"/> - <param name="max_isotope" value="3"/> - <param name="missed_cleavages" value="1"/> - <param name="number_of_hits" value="1"/> - <param name="estimate_precursor_mz" value="true"/> - <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="residue_set" value="Natural19WithoutI"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CompNovo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CompNovo_1_input.mzML"/> - <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="algorithm"> - <param name="max_number_aa_per_decomp" value="4"/> - <param name="tryptic_only" value="true"/> - <param name="precursor_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="max_number_pivot" value="9"/> - <param name="max_subscore_number" value="40"/> - <param name="decomp_weights_precision" value="0.01"/> - <param name="double_charged_iso_threshold" value="0.6"/> - <param name="max_mz" value="2000.0"/> - <param name="min_mz" value="200.0"/> - <param name="max_isotope_to_score" value="3"/> - <param name="max_decomp_weight" value="450.0"/> - <param name="max_isotope" value="3"/> - <param name="missed_cleavages" value="1"/> - <param name="number_of_hits" value="1"/> - <param name="estimate_precursor_mz" value="true"/> - <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="residue_set" value="Natural19WithoutI"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ConsensusID"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPMatrix"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="PAM30MS"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_2_input.featureXML"/> - <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="average"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_3_input.consensusXML"/> - <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPMatrix"/> - <section name="filter"> - <param name="considered_hits" value="6"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPIons"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.5"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_6_input.idXML"/> - <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="true"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="true"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_8_input.idXML"/> - <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="true"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="true"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ConsensusMapNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="accession_filter" value=""/> - <param name="description_filter" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="algorithm_type" value="robust_regression"/> - <param name="ratio_threshold" value="0.67"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CruxAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="custom_enzyme" value=""/> - <param name="decoy_prefix" value="decoy_"/> - <param name="deisotope" value="false"/> - <param name="report_decoys" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="extra_index_args" value=""/> - <param name="extra_search_args" value=""/> - <param name="extra_percolator_args" value=""/> - <param name="precursor_mass_tolerance" value="10.0"/> - <param name="precursor_mass_units" value="ppm"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="fragment_bin_width" value="0.02"/> - <param name="isotope_error" value=""/> - <param name="run_percolator" value="false"/> - <param name="enzyme" value="trypsin"/> - <param name="digestion" value="full-digest"/> - <param name="allowed_missed_cleavages" value="0"/> - <param name="decoy_format" value="peptide-reverse"/> - <param name="keep_terminal_aminos" value="NC"/> - <param name="cterm_modifications" value=""/> - <param name="nterm_modifications" value=""/> - <param name="modifications" value=""/> - <param name="test_fdr" value="0.01"/> - <param name="train_fdr" value="0.01"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CVInspector"> -</xml> - <xml name="autotest_DatabaseFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_1.fasta"/> - <param name="id" value="DatabaseFilter_1.idXML"/> - <param name="method" value="whitelist"/> - <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_1.fasta"/> - <param name="id" value="DatabaseFilter_1.idXML"/> - <param name="method" value="blacklist"/> - <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_3.fasta"/> - <param name="id" value="DatabaseFilter_3.mzid"/> - <param name="method" value="whitelist"/> - <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_3.fasta"/> - <param name="id" value="DatabaseFilter_3.mzid"/> - <param name="method" value="blacklist"/> - <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DatabaseSuitability"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="false"/> - <param name="reranking_cutoff_percentile" value="0.01"/> - <param name="FDR" value="0.8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="false"/> - <param name="reranking_cutoff_percentile" value="0.9"/> - <param name="FDR" value="1.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="true"/> - <param name="reranking_cutoff_percentile" value="0.01"/> - <param name="FDR" value="0.9"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_Decharger"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Decharger_input.featureXML"/> - <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <section name="FeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="10"/> - <param name="charge_span_max" value="4"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.1"/> - <param name="potential_adducts" value=""H:+:0.7" "Na:+:0.1" "(2)H4H-4:0:0.1:-2:heavy""/> - <param name="max_neutrals" value="0"/> - <param name="max_minority_bound" value="2"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DecoyDatabase"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="DECOY_"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="true"/> - <param name="type" value="protein"/> - <param name="method" value="reverse"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value=""/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="protein"/> - <param name="method" value="shuffle"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value="KRP"/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="protein"/> - <param name="method" value="shuffle"/> - <param name="enzyme" value="Chymotrypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value="KR"/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_4.fasta"/> - <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="RNA"/> - <param name="method" value="reverse"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value=""/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DeMeanderize"> -</xml> - <xml name="autotest_DigestorMotif"> -</xml> - <xml name="autotest_Digestor"> -</xml> - <xml name="autotest_DTAExtractor"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":"/> - <param name="rt" value=":61"/> - <param name="level" value="1,2,3"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":"/> - <param name="rt" value=":"/> - <param name="level" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":1000"/> - <param name="rt" value=":"/> - <param name="level" value="2"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_EICExtractor"> -</xml> - <xml name="autotest_Epifany"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idxml"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="true"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_input.consensusXML"/> - <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="true"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_input.consensusXML"/> - <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="false"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ERPairFinder"> -</xml> - <xml name="autotest_ExternalCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ExternalCalibration_1_input.mzML"/> - <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="offset" value="-5.5"/> - <param name="slope" value="0.0001"/> - <param name="power" value="0.0"/> - <param name="ms_level" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ExternalCalibration_1_input.mzML"/> - <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="offset" value="-5.5"/> - <param name="slope" value="0.0001"/> - <param name="power" value="0.0"/> - <param name="ms_level" value="2"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FalseDiscoveryRate"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="true"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="true"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="true"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_5_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="false"/> - <param name="protein" value="true"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="true"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_6_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="0.05"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_7_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="false"/> - <param name="protein" value="true"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="0.3"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderCentroided"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - <param name="pseudo_rt_shift" value="500.0"/> - </conditional> - <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> - <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="intensity"> - <param name="bins" value="1"/> - </section> - <section name="mass_trace"> - <param name="mz_tolerance" value="0.02"/> - <param name="min_spectra" value="14"/> - <param name="max_missing" value="1"/> - <param name="slope_bound" value="0.1"/> - </section> - <section name="isotopic_pattern"> - <param name="charge_low" value="2"/> - <param name="charge_high" value="2"/> - <param name="mz_tolerance" value="0.02"/> - <param name="intensity_percentage" value="10.0"/> - <param name="intensity_percentage_optional" value="0.1"/> - <param name="optional_fit_improvement" value="2.0"/> - <param name="mass_window_width" value="100.0"/> - <param name="abundance_12C" value="98.93"/> - <param name="abundance_14N" value="99.632"/> - </section> - <section name="seed"> - <param name="min_score" value="0.8"/> - </section> - <section name="fit"> - <param name="max_iterations" value="500"/> - </section> - <section name="feature"> - <param name="min_score" value="0.7"/> - <param name="min_isotope_fit" value="0.8"/> - <param name="min_trace_score" value="0.5"/> - <param name="min_rt_span" value="0.333"/> - <param name="max_rt_span" value="2.5"/> - <param name="rt_shape" value="symmetric"/> - <param name="max_intersection" value="0.35"/> - <param name="reported_mz" value="monoisotopic"/> - </section> - <section name="user-seed"> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.1"/> - <param name="min_score" value="0.5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderIdentification"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> - <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="batch_size" value="1000"/> - <param name="mz_window" value="0.1"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_quantile" value="0.95"/> - <param name="rt_window" value="0.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="60.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - <param name="mapping_tolerance" value="0.0"/> - </section> - <section name="svm"> - <param name="samples" value="0"/> - <param name="no_selection" value="false"/> - <param name="kernel" value="RBF"/> - <param name="xval" value="5"/> - <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> - <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> - <param name="epsilon" value="0.001"/> - <param name="cache_size" value="100.0"/> - <param name="no_shrinking" value="false"/> - <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> - <param name="min_prob" value="0.0"/> - </section> - <section name="model"> - <param name="type" value="none"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> - <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="batch_size" value="1000"/> - <param name="mz_window" value="0.1"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_quantile" value="0.95"/> - <param name="rt_window" value="0.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="60.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - <param name="mapping_tolerance" value="0.0"/> - </section> - <section name="svm"> - <param name="samples" value="0"/> - <param name="no_selection" value="false"/> - <param name="kernel" value="RBF"/> - <param name="xval" value="5"/> - <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> - <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> - <param name="epsilon" value="0.001"/> - <param name="cache_size" value="100.0"/> - <param name="no_shrinking" value="false"/> - <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> - <param name="min_prob" value="0.0"/> - </section> - <section name="model"> - <param name="type" value="symmetric"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderIsotopeWavelet"> -</xml> - <xml name="autotest_FeatureFinderMetaboIdent"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/> - <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/> - <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="mz_window" value="5.0"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_window" value="20.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="3.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - </section> - <section name="model"> - <param name="type" value="symmetric"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMetabo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="300.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="false"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="100.0"/> - <param name="chrom_peak_snr" value="0.0"/> - <param name="chrom_fwhm" value="100.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="median"/> - <param name="trace_termination_criterion" value="sample_rate"/> - <param name="trace_termination_outliers" value="2"/> - <param name="min_sample_rate" value="0.01"/> - <param name="min_trace_length" value="30.0"/> - <param name="max_trace_length" value="3000.0"/> - </section> - <section name="epd"> - <param name="enabled" value="false"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="10.0"/> - <param name="max_fwhm" value="80.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="4.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="false"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="false"/> - <param name="use_smoothed_intensities" value="false"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="fixed"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="fixed"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="true"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="max_height"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="300.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="false"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMRM"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMRM_1_input.mzML"/> - <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="min_rt_distance" value="10.0"/> - <param name="min_num_peaks_per_feature" value="5"/> - <param name="min_signal_to_noise_ratio" value="2.0"/> - <param name="write_debug_files" value="false"/> - <param name="resample_traces" value="false"/> - <param name="write_debuginfo" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMultiplex"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl8]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="90.0"/> - <param name="rt_band" value="10.0"/> - <param name="rt_min" value="5.0"/> - <param name="mz_tolerance" value="40.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10.0"/> - <param name="peptide_similarity" value="0.8"/> - <param name="averagine_similarity" value="0.75"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="1"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Lys8,Arg10]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="40.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[]"/> - <param name="charge" value="5:15"/> - <param name="isotopes_per_peptide" value="5:10"/> - <param name="rt_typical" value="45.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="200.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="RNA"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[]"/> - <param name="charge" value="5:15"/> - <param name="isotopes_per_peptide" value="5:10"/> - <param name="rt_typical" value="45.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="200.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="DNA"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="charge" value="1:5"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="3.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10000000.0"/> - <param name="peptide_similarity" value="0.95"/> - <param name="averagine_similarity" value="0.8"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="3"/> - <param name="spectrum_type" value="profile"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="charge" value="1:5"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="3.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10000000.0"/> - <param name="peptide_similarity" value="0.95"/> - <param name="averagine_similarity" value="0.8"/> - <param name="averagine_similarity_scaling" value="1.0"/> - <param name="missed_cleavages" value="3"/> - <param name="spectrum_type" value="profile"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Dimethyl4]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="40.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="2.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.75"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="31.0094"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> - <param name="charge" value="1:7"/> - <param name="isotopes_per_peptide" value="3:8"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="3.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10.0"/> - <param name="peptide_similarity" value="0.2"/> - <param name="averagine_similarity" value="0.25"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="4"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="true"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[0][6.03705]"/> - <param name="charge" value="2:8"/> - <param name="isotopes_per_peptide" value="3:8"/> - <param name="rt_typical" value="40.0"/> - <param name="rt_band" value="0.0"/> - <param name="rt_min" value="4.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.4"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="centroid"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="charge" value="1:7"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="50.0"/> - <param name="rt_band" value="5.0"/> - <param name="rt_min" value="8.0"/> - <param name="mz_tolerance" value="6.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="10.0"/> - <param name="peptide_similarity" value="0.4"/> - <param name="averagine_similarity" value="0.5"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="3"/> - <param name="spectrum_type" value="profile"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="true"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="labels" value="[]"/> - <param name="charge" value="1:4"/> - <param name="isotopes_per_peptide" value="3:6"/> - <param name="rt_typical" value="1e-05"/> - <param name="rt_band" value="0.0"/> - <param name="rt_min" value="0.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_unit" value="ppm"/> - <param name="intensity_cutoff" value="1000.0"/> - <param name="peptide_similarity" value="0.5"/> - <param name="averagine_similarity" value="0.7"/> - <param name="averagine_similarity_scaling" value="0.95"/> - <param name="missed_cleavages" value="0"/> - <param name="spectrum_type" value="automatic"/> - <param name="averagine_type" value="peptide"/> - <param name="knock_out" value="false"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderSuperHirn"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/> - <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="centroiding"> - <param name="active" value="false"/> - <param name="window_width" value="5"/> - <param name="absolute_isotope_mass_precision" value="0.01"/> - <param name="relative_isotope_mass_precision" value="10.0"/> - <param name="minimal_peak_height" value="0.0"/> - <param name="min_ms_signal_intensity" value="50.0"/> - </section> - <section name="ms1"> - <param name="precursor_detection_scan_levels" value="1"/> - <param name="max_inter_scan_distance" value="0"/> - <param name="tr_resolution" value="0.01"/> - <param name="intensity_threshold" value="1000.0"/> - <param name="max_inter_scan_rt_distance" value="0.1"/> - <param name="min_nb_cluster_members" value="4"/> - <param name="detectable_isotope_factor" value="0.05"/> - <param name="intensity_cv" value="0.9"/> - <param name="retention_time_tolerance" value="0.5"/> - <param name="mz_tolerance" value="0.0"/> - </section> - <section name="ms1_feature_merger"> - <param name="active" value="true"/> - <param name="tr_resolution" value="0.01"/> - <param name="initial_apex_tr_tolerance" value="5.0"/> - <param name="feature_merging_tr_tolerance" value="1.0"/> - <param name="intensity_variation_percentage" value="25.0"/> - <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> - </section> - <section name="ms1_feature_selection_options"> - <param name="start_elution_window" value="0.0"/> - <param name="end_elution_window" value="180.0"/> - <param name="mz_range_min" value="0.0"/> - <param name="mz_range_max" value="2000.0"/> - <param name="chrg_range_min" value="1"/> - <param name="chrg_range_max" value="5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/> - <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="centroiding"> - <param name="active" value="true"/> - <param name="window_width" value="5"/> - <param name="absolute_isotope_mass_precision" value="0.01"/> - <param name="relative_isotope_mass_precision" value="10.0"/> - <param name="minimal_peak_height" value="0.0"/> - <param name="min_ms_signal_intensity" value="50.0"/> - </section> - <section name="ms1"> - <param name="precursor_detection_scan_levels" value="1"/> - <param name="max_inter_scan_distance" value="0"/> - <param name="tr_resolution" value="0.01"/> - <param name="intensity_threshold" value="1000.0"/> - <param name="max_inter_scan_rt_distance" value="0.1"/> - <param name="min_nb_cluster_members" value="4"/> - <param name="detectable_isotope_factor" value="0.05"/> - <param name="intensity_cv" value="0.9"/> - <param name="retention_time_tolerance" value="0.5"/> - <param name="mz_tolerance" value="0.0"/> - </section> - <section name="ms1_feature_merger"> - <param name="active" value="true"/> - <param name="tr_resolution" value="0.01"/> - <param name="initial_apex_tr_tolerance" value="5.0"/> - <param name="feature_merging_tr_tolerance" value="1.0"/> - <param name="intensity_variation_percentage" value="25.0"/> - <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> - </section> - <section name="ms1_feature_selection_options"> - <param name="start_elution_window" value="0.0"/> - <param name="end_elution_window" value="180.0"/> - <param name="mz_range_min" value="0.0"/> - <param name="mz_range_max" value="2000.0"/> - <param name="chrg_range_min" value="1"/> - <param name="chrg_range_max" value="5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerLabeled"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> - <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="rt_estimate" value="false"/> - <param name="rt_pair_dist" value="-1.0"/> - <param name="rt_dev_low" value="0.4"/> - <param name="rt_dev_high" value="0.4"/> - <param name="mz_pair_dists" value="8.0"/> - <param name="mz_dev" value="0.1"/> - <param name="mrm" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/> - <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="rt_estimate" value="true"/> - <param name="rt_pair_dist" value="-121.0382"/> - <param name="rt_dev_low" value="123.3965"/> - <param name="rt_dev_high" value="123.3965"/> - <param name="mz_pair_dists" value="4.0"/> - <param name="mz_dev" value="0.1"/> - <param name="mrm" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeledKD"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="1"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="true"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="99999"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Identical"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Any"/> - <param name="adduct_merging" value="With_unknown_adducts"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Any"/> - <param name="adduct_merging" value="Identical"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeledQT"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="true"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="99999"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="true"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="true"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeled"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.5"/> - <param name="unit" value="Da"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.5"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="1.5"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="true"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.5"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FFEval"> -</xml> - <xml name="autotest_FidoAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="true"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="true"/> - <param name="group_level" value="true"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_4_input.idXML"/> - <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_5_input.idXML"/> - <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="true"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.9"/> - <param name="peptide" value="0.01"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_2_input.someInputDTA2D"/> - <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_3_input.featureXML"/> - <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_5_input.mzML"/> - <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_6_input.mzML"/> - <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_7_input.consensusXML"/> - <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_8_input.mzML"/> - <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/> - <param name="out_type" value="mzData"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_9_input.consensusXML"/> - <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_11_input.peplist"/> - <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> - <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_13_input.peptides.kroenik"/> - <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_9_output.featureXML"/> - <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="out_type" value="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="out_type" value="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_20_input.featureXML"/> - <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_23_input.mzML"/> - <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="true"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="true"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_26_output.mzXML"/> - <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="true"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_27_input.mzML"/> - <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="true"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_28_input.mzML"/> - <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="1e-05"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_29_output.mzML"/> - <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="multiple"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_30_input.mzML"/> - <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="single"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_30_output.mzML"/> - <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_32_input.mzML"/> - <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ginkgotoxin-ms-switching.raw"/> - <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":30"/> - <param name="mz" value=":1000"/> - <param name="int" value=":20000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value="30:"/> - <param name="mz" value="1000:"/> - <param name="int" value="100:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_4_input.mzML"/> - <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="true"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_5_input.featureXML"/> - <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value=":1000"/> - <param name="mz" value=":480"/> - <param name="int" value=":79000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":0.6"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":3"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_5_input.featureXML"/> - <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value="1000:"/> - <param name="mz" value="440:"/> - <param name="int" value="70000:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value="0.51:"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value="3:"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_7_input.mzML"/> - <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value="7000:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_8_input.consensusXML"/> - <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="rt" value="600:1400"/> - <param name="mz" value="700:2300"/> - <param name="int" value="1100:6000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_9_input.mzML"/> - <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value="SelectedIonMonitoring"/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_10_input.mzML"/> - <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value="Collision-induced dissociation"/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_11_input.mzML"/> - <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value="Plasma desorption"/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_12_input.mzML"/> - <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="true"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_13_input.consensusXML"/> - <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value="2"/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_14_input.consensusXML"/> - <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value="0 2"/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="true"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_18_input.consensusXML"/> - <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_18_input.consensusXML"/> - <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="true"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""YDL217C""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="true"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="true"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""distinct_charges" "gt" "1,2""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""distinct_charges_size" "gt" "2""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""DOESNOTEXIST" "lt" "whatever""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_25_input.mzML.gz"/> - <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="blacklist" value="FileFilter_25_input.idXML"/> - <param name="rt" value="1.0"/> - <param name="mz" value="0.05"/> - <param name="blacklist_imperfect" value="true"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_25_input.mzML.gz"/> - <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="blacklist" value="FileFilter_25_input.idXML"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="true"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":2"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":2"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":35"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":35"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="false"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="intensity" value="slof"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="intensity" value="pic"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value="positive"/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value="negative"/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_43_input.mzML"/> - <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_43.tmp.mzML"/> - <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_44_input.mzML"/> - <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_45_input.featureXML"/> - <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_46_input.featureXML"/> - <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> - <param name="sequence_comparison_method" value="exact"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_47_input.mzML"/> - <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="file" value="FileFilter_47_input_select.mzML"/> - <param name="similarity_threshold" value="0.9"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_47_input.mzML"/> - <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="file" value="FileFilter_47_input_select.mzML"/> - <param name="similarity_threshold" value="0.9"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="false"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_49_input.mzML"/> - <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="true"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="pic"/> - <param name="float_da" value="slof"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileInfo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> - <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> - <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_3_input.featureXML"/> - <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_4_input.mzXML"/> - <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_5_input.mzDat"/> - <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="false"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_6_input.mzData"/> - <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="true"/> - <param name="d" value="true"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_7_input.consensusXML"/> - <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_9_input.mzML"/> - <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_10_input.idXML"/> - <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_12_input.mzML"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_13_input.consensusXML"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_14_input.mzid"/> - <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="true"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_15_input.mzid"/> - <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="true"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_16_input.trafoXML"/> - <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_17_input.fasta"/> - <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_18_input.fasta"/> - <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileMerger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value="5.0 10.0"/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="true"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="true"/> - <param name="ms_level" value="2"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/> - <param name="out_type" value="featureXML"/> - <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> - <param name="out_type" value="consensusXML"/> - <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/> - <param name="out_type" value="traML"/> - <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="10.0"/> - </section> - <output_collection name="rt_concat_trafo_out" count="2"/> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> - <param name="out_type" value="consensusXML"/> - <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_cols"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FuzzyDiff"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="whitelist" value=""<?xml-stylesheet""/> - <param name="matched_whitelist" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> - <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> - <param name="ratio" value="1.01"/> - <param name="absdiff" value="0.01"/> - <param name="verbose" value="1"/> - <param name="tab_width" value="8"/> - <param name="first_column" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_GNPSExport"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_single.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML"/> - <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_single.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML"/> - <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="merged_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_merged.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> - <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_merged.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> - <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_HighResPrecursorMassCorrector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="4"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.2"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDConflictResolver"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_1_input.featureXML"/> - <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_2_input.consensusXML"/> - <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_3_input.consensusXML"/> - <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_4_input.featureXML"/> - <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="resolve_between_features" value="highest_intensity"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDExtractor"> -</xml> - <xml name="autotest_IDFileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_1_input1.mascotXML"/> - <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PepXMLFile_test.pepxml"/> - <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="PepXMLFile_test.mzML"/> - <param name="mz_name" value="PepXMLFile_test"/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_3_input.protXML"/> - <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value="scan=(?<SCAN>\d+)"/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_1_input1.mascotXML"/> - <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_6_input1.pepXML"/> - <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value="F025589.dat.mzML"/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_7_input1.xml"/> - <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_8_input.mzid"/> - <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_9_input.idXML"/> - <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <param name="out_type" value="mzid"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_10_input.pepXML"/> - <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> - <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="PEP"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="score"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> - <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="spectra.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_16_input.pepXML"/> - <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_17_input.idXML"/> - <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_18_input.idXML"/> - <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_19_input.idXML"/> - <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_20_input.idXML"/> - <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_21_input.idXML"/> - <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDMapper_4_input.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.01"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> - <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="spectra.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_23_input.mzid"/> - <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_24_input.pep.xml"/> - <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_25_input.idXML"/> - <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_26_input.mzid"/> - <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="-1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="true"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="true"/> - <param name="number_of_hits" value="2"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_31_input.mzid"/> - <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_1_input.idXML"/> - <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="proteins" value="IDFilter_1_input.fas"/> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_3_input.idXML"/> - <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="peptides" value="IDFilter_3_2_input.idXML"/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_4_input.idXML"/> - <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.08"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="32.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="32.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_6_input.idXML"/> - <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="2"/> - <param name="n_protein_hits" value="10"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="true"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_7_input.idXML"/> - <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_8_input.idXML"/> - <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value="200:350"/> - <param name="mz" value="999:1000"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_9_input.idXML"/> - <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.05"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_10_input.idXML"/> - <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.3"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_11_input.idXML"/> - <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="true"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_12_input.idXML"/> - <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_12_input.fasta"/> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_13_input.idXML"/> - <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_13_input.fasta"/> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_14_input.idXML"/> - <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_14_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_15_input.idXML"/> - <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_15_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="semi"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_16_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="true"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":2"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="2:"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="1:3"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="1:0"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""calcMZ" "gt" "750.0""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""end" "ne" "23""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_2_output.consensusXML"/> - <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""Q9HP81""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_3_out.consensusXML"/> - <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.99"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMapper"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_1_input.idXML"/> - <param name="in" value="IDMapper_1_input.featureXML"/> - <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.0"/> - <param name="mz_measure" value="Da"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_2_input.idXML"/> - <param name="in" value="IDMapper_2_input.consensusXML"/> - <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.0"/> - <param name="mz_measure" value="Da"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_3_input.idXML"/> - <param name="in" value="IDMapper_3_input.featureXML"/> - <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="4.0"/> - <param name="mz_tolerance" value="3.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_4_input.idXML"/> - <param name="in" value="IDMapper_4_input.featureXML"/> - <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="10.0"/> - <param name="mz_tolerance" value="20.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_4_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_5_input.idXML"/> - <param name="in" value="IDMapper_5_input.featureXML"/> - <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="20.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_5_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMassAccuracy"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="number_of_bins" value="10"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/> - <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_error_ppm" value="false"/> - <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_error_ppm" value="false"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMerger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/> - <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="true"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/> - <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="true"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/> - <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/> - <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_2_input1.idXML"/> - <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="add_to" value="IDMerger_5_input1.idXML"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/> - <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="true"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDPosteriorErrorProbability"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="true"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="true"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDRipper"/> - <xml name="autotest_IDRTCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRTCalibration_1_input.idXML"/> - <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="calibrant_1_reference" value="0.1"/> - <param name="calibrant_2_reference" value="0.9"/> - <param name="calibrant_1_input" value="10.0"/> - <param name="calibrant_2_input" value="90.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="degenerated_empty.idXML"/> - <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="calibrant_1_reference" value="0.1"/> - <param name="calibrant_2_reference" value="0.9"/> - <param name="calibrant_1_input" value="10.0"/> - <param name="calibrant_2_input" value="90.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDScoreSwitcher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_output.idXML"/> - <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="proteins" value="false"/> - <param name="new_score" value="Percolator_PEP"/> - <param name="new_score_orientation" value="lower_better"/> - <param name="new_score_type" value="Posterior Error Probability"/> - <param name="old_score" value="Percolator_qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDScoreSwitcher_2_input.idXML"/> - <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="proteins" value="true"/> - <param name="new_score" value="Posterior Probability_score"/> - <param name="new_score_orientation" value="higher_better"/> - <param name="new_score_type" value="Posterior Probability"/> - <param name="old_score" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDSplitter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_1_output.featureXML"/> - <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_InternalCalibration"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="InternalCalibration_1_BSA1.mzML"/> - <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ppm_match_tolerance" value="25.0"/> - <param name="ms_level" value="1"/> - <param name="RT_chunking" value="-1.0"/> - <section name="cal"> - <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/> - <param name="lock_require_mono" value="false"/> - <param name="lock_require_iso" value="false"/> - <param name="model_type" value="linear"/> - </section> - <section name="RANSAC"> - <param name="enabled" value="true"/> - <param name="threshold" value="1.0"/> - <param name="pc_inliers" value="30"/> - <param name="iter" value="500"/> - </section> - <section name="goodness"> - <param name="median" value="4.0"/> - <param name="MAD" value="2.0"/> - </section> - <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> - <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ppm_match_tolerance" value="25.0"/> - <param name="ms_level" value="1 2 3"/> - <param name="RT_chunking" value="60.0"/> - <section name="cal"> - <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/> - <param name="lock_require_mono" value="true"/> - <param name="lock_require_iso" value="false"/> - <param name="model_type" value="linear"/> - </section> - <section name="RANSAC"> - <param name="enabled" value="false"/> - <param name="threshold" value="10.0"/> - <param name="pc_inliers" value="30"/> - <param name="iter" value="70"/> - </section> - <section name="goodness"> - <param name="median" value="4.0"/> - <param name="MAD" value="2.0"/> - </section> - <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IsobaricAnalyzer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> - <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value=""/> - <param name="reporter_mass_shift" value="0.1"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value="l1"/> - <param name="channel_115_description" value="l2"/> - <param name="channel_116_description" value="l3"/> - <param name="channel_117_description" value="lung"/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="TMTTenPlexMethod_test.mzML"/> - <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="High-energy collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="TMTTenPlexMethod_test.mzML"/> - <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="High-energy collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="tmt10plex"/> - <param name="in" value="MS3_nonHierarchical.mzML"/> - <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="Collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_LabeledEval"> -</xml> - <xml name="autotest_LuciphorAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="LuciphorAdapter_1_input.mzML"/> - <param name="id" value="LuciphorAdapter_1_input.idXML"/> - <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="fragment_method" value="CID"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <param name="fragment_error_units" value="Da"/> - <param name="min_mz" value="150.0"/> - <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> - <param name="neutral_losses" value=""sty -H3PO4 -97.97690""/> - <param name="decoy_mass" value="79.966331"/> - <param name="decoy_neutral_losses" value=""X -H3PO4 -97.97690""/> - <param name="max_charge_state" value="5"/> - <param name="max_peptide_length" value="40"/> - <param name="max_num_perm" value="16384"/> - <param name="modeling_score_threshold" value="0.95"/> - <param name="scoring_threshold" value="0.0"/> - <param name="min_num_psms_model" value="1"/> - <param name="run_mode" value="0"/> - <param name="rt_tolerance" value="0.01"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerIdentification"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="1"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="2"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="trafo_out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_7_input1.idXML"/> - <output_collection name="out" count="1"/> - <output_collection name="trafo_out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_7_input2.idXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerPoseClustering"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <output_collection name="trafo_out" count="3"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/> - <output_collection name="out" count="3"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/> - <output_collection name="trafo_out" count="2"/> - <section name="reference"> - <param name="index" value="2"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerSpectrum"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="gapcost" value="1.0"/> - <param name="affinegapcost" value="0.5"/> - <param name="cutoff_score" value="0.7"/> - <param name="bucketsize" value="100"/> - <param name="anchorpoints" value="100"/> - <param name="mismatchscore" value="-5.0"/> - <param name="scorefunction" value="SteinScottImproveScore"/> - </section> - <section name="model"> - <param name="type" value="interpolated"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerTreeGuided"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="trafo_out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_input.mzML"/> - <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapRTTransformer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_2_input.mzML"/> - <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/> - <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="invert" value="true"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/> - <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="true"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapStatistics"> -</xml> - <xml name="autotest_MaRaClusterAdapter"/> - <xml name="autotest_MascotAdapterOnline"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_protein_links" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="Mascot_parameters"> - <param name="database" value="SwissProt"/> - <param name="search_type" value="MIS"/> - <param name="enzyme" value="Trypsin"/> - <param name="instrument" value="Default"/> - <param name="missed_cleavages" value="1"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="Da"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="fragment_error_units" value="Da"/> - <param name="charges" value="1,2,3"/> - <param name="taxonomy" value="All entries"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/> - <param name="mass_type" value="monoisotopic"/> - <param name="number_of_hits" value="0"/> - <param name="skip_spectrum_charges" value="false"/> - <param name="search_title" value="OpenMS_search"/> - <param name="username" value="OpenMS"/> - <param name="email" value="openmsjenkins@gmail.com"/> - </section> - <section name="Mascot_server"> - <param name="hostname" value="www.matrixscience.com"/> - <param name="host_port" value="80"/> - <param name="server_path" value=""/> - <param name="timeout" value="1500"/> - <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/> - <param name="use_proxy" value="false"/> - <param name="proxy_host" value=""/> - <param name="proxy_port" value="0"/> - <param name="proxy_username" value=""/> - <param name="proxy_password" value=""/> - <param name="login" value="false"/> - <param name="username" value=""/> - <param name="password" value=""/> - <param name="use_ssl" value="false"/> - <param name="export_params" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0"/> - <param name="skip_export" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MascotAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MascotAdapter_1_input.mzData"/> - <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/> - <param name="out_type" value="mgf"/> - <param name="instrument" value="ESI-TRAP"/> - <param name="precursor_mass_tolerance" value="1.3"/> - <param name="peak_mass_tolerance" value="0.3"/> - <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> - <param name="modifications" value=""Carboxymethyl (C)""/> - <param name="variable_modifications" value=""Variable_Modifications_TEST_1""/> - <param name="charges" value=""1+" "2+" "3+""/> - <param name="db" value="MSDB"/> - <param name="hits" value="AUTO"/> - <param name="cleavage" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="sig_threshold" value="0.05"/> - <param name="pep_homol" value="1.0"/> - <param name="pep_ident" value="1.0"/> - <param name="pep_rank" value="1"/> - <param name="prot_score" value="1.0"/> - <param name="pep_score" value="1.0"/> - <param name="pep_exp_z" value="1"/> - <param name="show_unassigned" value="1"/> - <param name="first_dim_rt" value="0.0"/> - <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/> - <param name="mass_type" value="Monoisotopic"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MascotAdapter_2_input.mascotXML"/> - <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="instrument" value="Default"/> - <param name="precursor_mass_tolerance" value="2.0"/> - <param name="peak_mass_tolerance" value="1.0"/> - <param name="taxonomy" value="All entries"/> - <param name="modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="charges" value=""1+" "2+" "3+""/> - <param name="db" value="MSDB"/> - <param name="hits" value="AUTO"/> - <param name="cleavage" value="Trypsin"/> - <param name="missed_cleavages" value="0"/> - <param name="sig_threshold" value="0.05"/> - <param name="pep_homol" value="1.0"/> - <param name="pep_ident" value="1.0"/> - <param name="pep_rank" value="1"/> - <param name="prot_score" value="1.0"/> - <param name="pep_score" value="1.0"/> - <param name="pep_exp_z" value="1"/> - <param name="show_unassigned" value="1"/> - <param name="first_dim_rt" value="0.0"/> - <param name="boundary" value=""/> - <param name="mass_type" value="Monoisotopic"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MassCalculator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/> - <param name="in_seq" value=""/> - <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="charge" value="0 1"/> - <param name="format" value="table"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=","/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> - <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="charge" value="1 2 3"/> - <param name="format" value="list"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MassTraceExtractor"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassTraceExtractor_1_input.mzML"/> - <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - <param name="enabled" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassTraceExtractor_1_input.mzML"/> - <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="6.0"/> - <param name="max_trace_length" value="12.0"/> - </section> - <section name="epd"> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - <param name="enabled" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MetaboliteAdductDecharger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> - <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="MetaboliteFeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="3"/> - <param name="charge_span_max" value="3"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.05"/> - <param name="unit" value="Da"/> - <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> - <param name="max_neutrals" value="1"/> - <param name="use_minority_bound" value="true"/> - <param name="max_minority_bound" value="3"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> - <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <section name="MetaboliteFeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="3"/> - <param name="charge_span_max" value="3"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.05"/> - <param name="unit" value="Da"/> - <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> - <param name="max_neutrals" value="1"/> - <param name="use_minority_bound" value="true"/> - <param name="max_minority_bound" value="3"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MetaboliteSpectralMatcher"> -</xml> - <xml name="autotest_MetaProSIP"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_correlation_distance_to_averagine" value="-1.0"/> - <param name="pattern_15N_TIC_threshold" value="0.95"/> - <param name="pattern_13C_TIC_threshold" value="0.95"/> - <param name="pattern_2H_TIC_threshold" value="0.95"/> - <param name="pattern_18O_TIC_threshold" value="0.95"/> - <param name="heatmap_bins" value="20"/> - <param name="observed_peak_fraction" value="0.5"/> - <param name="min_consecutive_isotopes" value="2"/> - <param name="score_plot_yaxis_min" value="0.0"/> - <param name="collect_method" value="correlation_maximum"/> - <param name="lowRIA_correlation_threshold" value="-1.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_mzML" value="MetaProSIP_1_input.mzML"/> - <param name="in_fasta" value="MetaProSIP_1_input.fasta"/> - <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/> - <param name="mz_tolerance_ppm" value="10.0"/> - <param name="rt_tolerance_s" value="30.0"/> - <param name="intensity_threshold" value="10.0"/> - <param name="correlation_threshold" value="0.7"/> - <param name="xic_threshold" value="0.7"/> - <param name="decomposition_threshold" value="0.7"/> - <param name="weight_merge_window" value="5.0"/> - <param name="plot_extension" value="png"/> - <param name="qc_output_directory" value=""/> - <param name="labeling_element" value="C"/> - <param name="use_unassigned_ids" value="false"/> - <param name="use_averagine_ids" value="false"/> - <param name="report_natural_peptides" value="false"/> - <param name="filter_monoisotopic" value="false"/> - <param name="cluster" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MRMMapper"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMMapping_input.chrom.mzML"/> - <param name="tr" value="MRMMapping_input.TraML"/> - <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="precursor_tolerance" value="0.3"/> - <param name="product_tolerance" value="0.3"/> - <param name="map_multiple_assays" value="false"/> - <param name="error_on_unmapped" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMMapping_input.chrom.mzML"/> - <param name="tr" value="MRMMapping_input_2.TraML"/> - <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="precursor_tolerance" value="0.01"/> - <param name="product_tolerance" value="0.01"/> - <param name="map_multiple_assays" value="false"/> - <param name="error_on_unmapped" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MRMPairFinder"> -</xml> - <xml name="autotest_MRMTransitionGroupPicker"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> - <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> - <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="true"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MSFraggerAdapter"/> - <xml name="autotest_MSGFPlusAdapter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="add_decoys" value="false"/> - <param name="legacy_conversion" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <param name="database" value="proteins.fasta"/> - <param name="precursor_mass_tolerance" value="10.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error_range" value="0,1"/> - <param name="fragment_method" value="from_spectrum"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="protocol" value="none"/> - <param name="tryptic" value="fully"/> - <param name="min_precursor_charge" value="1"/> - <param name="max_precursor_charge" value="3"/> - <param name="min_peptide_length" value="6"/> - <param name="max_peptide_length" value="40"/> - <param name="matches_per_spec" value="1"/> - <param name="add_features" value="false"/> - <param name="max_mods" value="2"/> - <param name="max_missed_cleavages" value="-1"/> - <param name="tasks" value="0"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MSSimulator"> -</xml> - <xml name="autotest_MSstatsConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="max"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_1_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/> - <param name="method" value="LFQ"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="manual"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_2_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/> - <param name="method" value="ISO"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="manual"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_3_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/> - <param name="method" value="ISO"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MultiplexResolver"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_1_input.consensusXML"/> - <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> - <param name="missed_cleavages" value="1"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_2_input.consensusXML"/> - <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> - <param name="missed_cleavages" value="4"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_3_input.consensusXML"/> - <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Leu3]"/> - <param name="missed_cleavages" value="2"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_4_input.consensusXML"/> - <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> - <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="missed_cleavages" value="3"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="10"/> - </section> - <section name="labels"> - <param name="Arg6" value="6.0201290268"/> - <param name="Arg10" value="10.0082686"/> - <param name="Lys4" value="4.0251069836"/> - <param name="Lys6" value="6.0201290268"/> - <param name="Lys8" value="8.0141988132"/> - <param name="Leu3" value="3.01883"/> - <param name="Dimethyl0" value="28.0313"/> - <param name="Dimethyl4" value="32.056407"/> - <param name="Dimethyl6" value="34.063117"/> - <param name="Dimethyl8" value="36.07567"/> - <param name="ICPL0" value="105.021464"/> - <param name="ICPL4" value="109.046571"/> - <param name="ICPL6" value="111.041593"/> - <param name="ICPL10" value="115.0667"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MyriMatchAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="MinPeptideMass" value="0.0"/> - <param name="MaxPeptideMass" value="10000.0"/> - <param name="MinPeptideLength" value="5"/> - <param name="MaxPeptideLength" value="75"/> - <param name="UseSmartPlusThreeModel" value="false"/> - <param name="NumIntensityClasses" value="3"/> - <param name="ClassSizeMultiplier" value="2.0"/> - <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/> - <param name="SpectrumListFilters" value=""/> - <param name="ignoreConfigErrors" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_mass_tolerance_unit" value="ppm"/> - <param name="precursor_mass_tolerance_avg" value="false"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance_unit" value="Da"/> - <param name="database" value="proteins.fasta"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="NumChargeStates" value="3"/> - <param name="TicCutoffPercentage" value="0.98"/> - <param name="MaxDynamicMods" value="2"/> - <param name="MaxResultRank" value="5"/> - <param name="CleavageRules" value=""/> - <param name="MinTerminiCleavages" value="2"/> - <param name="MaxMissedCleavages" value="-1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MzMLSplitter"/> - <xml name="autotest_MzTabExporter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_1_input.consensusXML"/> - <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_2_input.idXML"/> - <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_3_input.featureXML"/> - <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_out.consensusXML"/> - <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_5_in.consensusXML"/> - <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_6_input.idXML"/> - <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_7_input.consensusXML"/> - <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NoiseFilterGaussian"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="1.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="50.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="1.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="50.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NoiseFilterSGolay"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> - <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="9"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="11"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> - <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="9"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="11"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NovorAdapter"/> - <xml name="autotest_NucleicAcidSearchEngine"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="decharge_ms2" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> - <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> - <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="-2"/> - <param name="max_charge" value="-14"/> - <param name="include_unknown_charge" value="true"/> - <param name="use_avg_mass" value="false"/> - <param name="use_adducts" value="false"/> - <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> - <param name="isotopes" value="0 1 2"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="ions" value="a-B,c,w,y"/> - </section> - <section name="modifications"> - <param name="variable" value=""/> - <param name="variable_max_per_oligo" value="2"/> - <param name="resolve_ambiguities" value="false"/> - </section> - <section name="oligo"> - <param name="min_size" value="5"/> - <param name="max_size" value="0"/> - <param name="missed_cleavages" value="22"/> - <param name="enzyme" value="no cleavage"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="fdr"> - <param name="decoy_pattern" value="DECOY_"/> - <param name="cutoff" value="0.05"/> - <param name="remove_decoys" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OMSSAAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="pc" value="1"/> - <param name="hs" value="4"/> - <param name="tez" value="1"/> - <param name="tom" value="0"/> - <param name="tem" value="0"/> - <param name="tex" value="1446.94"/> - <param name="zt" value="3"/> - <param name="z1" value="0.95"/> - <param name="zc" value="1"/> - <param name="zcc" value="2"/> - <param name="zoh" value="2"/> - <param name="no" value="4"/> - <param name="nox" value="40"/> - <param name="i" value="1,4"/> - <param name="sp" value="100"/> - <param name="sb1" value="1"/> - <param name="sct" value="0"/> - <param name="x" value="0"/> - <param name="hm" value="2"/> - <param name="ht" value="6"/> - <param name="mm" value="128"/> - <param name="mnm" value="false"/> - <param name="is" value="0.0"/> - <param name="ir" value="0.0"/> - <param name="ii" value="0.0"/> - <param name="chunk_size" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="database" value="proteins.fasta"/> - <param name="min_precursor_charge" value="1"/> - <param name="max_precursor_charge" value="3"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="v" value="1"/> - <param name="enzyme" value="Trypsin"/> - <param name="hl" value="30"/> - <param name="he" value="1.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenPepXLLF"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXLLF_input.mzML"/> - <param name="database" value="OpenPepXLLF_input.fasta"/> - <param name="decoy_string" value="decoy"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="2 1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_xlinks" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="2"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""K" "N-term""/> - <param name="residue2" value=""K" "N-term""/> - <param name="mass" value="138.0680796"/> - <param name="mass_mono_link" value="156.07864431 155.094628715"/> - <param name="name" value="DSS"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="5"/> - <param name="deisotope" value="auto"/> - <param name="use_sequence_tags" value="false"/> - <param name="sequence_tag_min_length" value="2"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXLLF_input2.mzML"/> - <param name="database" value="OpenPepXLLF_input2.fasta"/> - <param name="decoy_string" value="decoy_"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.2"/> - <param name="mass_tolerance_xlinks" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value="Carbamidomethyl (C)"/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="1"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""D" "E" "C-term""/> - <param name="residue2" value=""K" "S" "T" "Y" "N-term""/> - <param name="mass" value="-18.010595"/> - <param name="mass_mono_link" value=""/> - <param name="name" value="DMTMM"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="1"/> - <param name="deisotope" value="auto"/> - <param name="use_sequence_tags" value="false"/> - <param name="sequence_tag_min_length" value="2"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenPepXL"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXL_input.mzML"/> - <param name="consensus" value="OpenPepXL_input.consensusXML"/> - <param name="database" value="OpenPepXL_input.fasta"/> - <param name="decoy_string" value="decoy"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="2 1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.2"/> - <param name="mass_tolerance_xlinks" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="2"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""K" "N-term""/> - <param name="residue2" value=""K" "N-term""/> - <param name="mass_light" value="138.0680796"/> - <param name="mass_iso_shift" value="12.075321"/> - <param name="mass_mono_link" value="156.07864431 155.094628715"/> - <param name="name" value="DSS"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="5"/> - <param name="deisotope" value="auto"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathAnalyzer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="8.0"/> - <param name="dia_byseries_ppm_diff" value="15.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="8.0"/> - <param name="dia_byseries_ppm_diff" value="15.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="original"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathAssayGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="2,3"/> - <param name="enable_detection_specific_losses" value="true"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="enable_ipf" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/> - <param name="enable_ipf" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/> - <param name="enable_ipf" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathChromatogramExtractor"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="50.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="true"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="true"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="true"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathConfidenceScoring"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> - <param name="decoys" value="1"/> - <param name="transitions" value="2"/> - <section name="GLM"> - <param name="intercept" value="3.87333466"/> - <param name="delta_rt" value="-0.02898629"/> - <param name="dist_int" value="-7.75880768"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathDecoyGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.8"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.4"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="true"/> - <param name="enable_detection_unspecific_losses" value="true"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> - <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathDIAPreScoring"> -</xml> - <xml name="autotest_OpenSwathFeatureXMLToTSV"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="true"/> - <param name="best_scoring_peptide" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="false"/> - <param name="best_scoring_peptide" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="true"/> - <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathFileSplitter"/> - <xml name="autotest_OpenSwathMzMLFileCacher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="out_type" value="sqmass"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> - <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="out_type" value="sqmass"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> - <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> - <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="false"/> - <param name="full_meta" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathRewriteToFeatureXML"> -</xml> - <xml name="autotest_OpenSwathRTNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="false"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="true"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="3"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="3"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="false"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathWorkflow"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> - <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cache"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cacheWorkingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="true"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/> - <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="550.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_11_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/> - <param name="tr_type" value=""/> - <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/> - <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="true"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.2"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="none"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="true"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/> - <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="sqMass"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/> - <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="2"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_15_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="true"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="2"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="true"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cache"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="true"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_21_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/> - <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.6666666666666666"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="true"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_22_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerHiRes"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_input.mzML"/> - <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_2_input.mzML"/> - <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_input.mzML"/> - <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_2_input.mzML"/> - <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_5_input.mzML"/> - <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="0.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value=""/> - <param name="report_FWHM" value="false"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerIterative"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerIterative_1_input.mzML"/> - <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise_" value="1.0"/> - <param name="peak_width" value="0.04"/> - <param name="spacing_difference" value="1.5"/> - <param name="sn_bin_count_" value="30"/> - <param name="nr_iterations_" value="5"/> - <param name="sn_win_len_" value="20.0"/> - <param name="check_width_internally" value="false"/> - <param name="ms1_only" value="false"/> - <param name="clear_meta_data" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerIterative_2_input.mzML"/> - <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise_" value="0.0"/> - <param name="peak_width" value="0.04"/> - <param name="spacing_difference" value="2.5"/> - <param name="sn_bin_count_" value="30"/> - <param name="nr_iterations_" value="5"/> - <param name="sn_win_len_" value="20.0"/> - <param name="check_width_internally" value="true"/> - <param name="ms1_only" value="false"/> - <param name="clear_meta_data" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerWavelet"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/> - <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="2.0"/> - <param name="centroid_percentage" value="0.8"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="1.0"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="200.0"/> - <param name="peak_bound_ms2_level" value="50.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="true"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.1"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="100"/> - <section name="penalties"> - <param name="position" value="1.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PepNovoAdapter"> -</xml> - <xml name="autotest_PeptideIndexer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="true"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="0"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_2.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="3"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="full"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="semi"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="remove"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_10_input.idXML"/> - <param name="fasta" value="PeptideIndexer_10_input.fasta"/> - <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="3"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="true"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="auto"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="empty.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="auto"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_14.idXML"/> - <param name="fasta" value="PeptideIndexer_2.fasta"/> - <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PercolatorAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.5"/> - <param name="trainFDR" value="0.5"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PercolatorAdapter_1.idXML"/> - <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_2.osw"/> - <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms1"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/> - <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/> - <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="transition"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.5"/> - <param name="trainFDR" value="0.5"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PercolatorAdapter_1.idXML"/> - <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="idXML"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PhosphoScoring"> -</xml> - <xml name="autotest_PrecursorIonSelector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="solver" value="GLPK"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorIonSelector_features.featureXML"/> - <param name="ids" value="PrecursorIonSelector_ids.idXML"/> - <param name="num_precursors" value="1"/> - <param name="load_preprocessing" value="false"/> - <param name="store_preprocessing" value="false"/> - <param name="simulation" value="true"/> - <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="db_path" value="PrecursorIonSelector_db.fasta"/> - <param name="fixed_modifications" value=""/> - <section name="algorithm"> - <param name="type" value="IPS"/> - <param name="max_iteration" value="10"/> - <param name="rt_bin_capacity" value="10"/> - <param name="step_size" value="1"/> - <param name="peptide_min_prob" value="0.2"/> - <param name="sequential_spectrum_order" value="false"/> - <section name="MIPFormulation"> - <section name="thresholds"> - <param name="min_protein_probability" value="0.2"/> - <param name="min_protein_id_probability" value="0.95"/> - <param name="min_pt_weight" value="0.5"/> - <param name="min_mz" value="500.0"/> - <param name="max_mz" value="5000.0"/> - <param name="min_pred_pep_prob" value="0.5"/> - <param name="min_rt_weight" value="0.5"/> - <param name="use_peptide_rule" value="true"/> - <param name="min_peptide_ids" value="2"/> - <param name="min_peptide_probability" value="0.95"/> - </section> - <section name="combined_ilp"> - <param name="k1" value="0.2"/> - <param name="k2" value="0.2"/> - <param name="k3" value="0.4"/> - <param name="scale_matching_probs" value="true"/> - </section> - <section name="feature_based"> - <param name="no_intensity_normalization" value="false"/> - <param name="max_number_precursors_per_feature" value="1"/> - </section> - </section> - <section name="Preprocessing"> - <param name="precursor_mass_tolerance" value="0.9"/> - <param name="precursor_mass_tolerance_unit" value="Da"/> - <param name="preprocessed_db_path" value=""/> - <param name="preprocessed_db_pred_rt_path" value=""/> - <param name="preprocessed_db_pred_dt_path" value=""/> - <param name="max_peptides_per_run" value="100000"/> - <param name="missed_cleavages" value="1"/> - <param name="taxonomy" value=""/> - <param name="store_peptide_sequences" value="false"/> - <section name="rt_settings"> - <param name="min_rt" value="960.0"/> - <param name="max_rt" value="3840.0"/> - <param name="rt_step_size" value="30.0"/> - <param name="gauss_mean" value="-1.0"/> - <param name="gauss_sigma" value="3.0"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="solver" value="GLPK"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorIonSelector_features.featureXML"/> - <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="ids" value="PrecursorIonSelector_ids.idXML"/> - <param name="num_precursors" value="1"/> - <param name="load_preprocessing" value="false"/> - <param name="store_preprocessing" value="false"/> - <param name="simulation" value="false"/> - <param name="db_path" value="PrecursorIonSelector_db.fasta"/> - <param name="fixed_modifications" value=""/> - <section name="algorithm"> - <param name="type" value="IPS"/> - <param name="max_iteration" value="10"/> - <param name="rt_bin_capacity" value="10"/> - <param name="step_size" value="1"/> - <param name="peptide_min_prob" value="0.2"/> - <param name="sequential_spectrum_order" value="false"/> - <section name="MIPFormulation"> - <section name="thresholds"> - <param name="min_protein_probability" value="0.2"/> - <param name="min_protein_id_probability" value="0.95"/> - <param name="min_pt_weight" value="0.5"/> - <param name="min_mz" value="500.0"/> - <param name="max_mz" value="5000.0"/> - <param name="min_pred_pep_prob" value="0.5"/> - <param name="min_rt_weight" value="0.5"/> - <param name="use_peptide_rule" value="true"/> - <param name="min_peptide_ids" value="2"/> - <param name="min_peptide_probability" value="0.95"/> - </section> - <section name="combined_ilp"> - <param name="k1" value="0.2"/> - <param name="k2" value="0.2"/> - <param name="k3" value="0.4"/> - <param name="scale_matching_probs" value="true"/> - </section> - <section name="feature_based"> - <param name="no_intensity_normalization" value="false"/> - <param name="max_number_precursors_per_feature" value="1"/> - </section> - </section> - <section name="Preprocessing"> - <param name="precursor_mass_tolerance" value="0.9"/> - <param name="precursor_mass_tolerance_unit" value="Da"/> - <param name="preprocessed_db_path" value=""/> - <param name="preprocessed_db_pred_rt_path" value=""/> - <param name="preprocessed_db_pred_dt_path" value=""/> - <param name="max_peptides_per_run" value="100000"/> - <param name="missed_cleavages" value="1"/> - <param name="taxonomy" value=""/> - <param name="store_peptide_sequences" value="false"/> - <section name="rt_settings"> - <param name="min_rt" value="960.0"/> - <param name="max_rt" value="3840.0"/> - <param name="rt_step_size" value="30.0"/> - <param name="gauss_mean" value="-1.0"/> - <param name="gauss_sigma" value="3.0"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PrecursorMassCorrector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_charge" value="3"/> - <param name="intensity_threshold" value="-1.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> - <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="precursor_mass_tolerance" value="1.5"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinInference"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinInference_1_input.idXML"/> - <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="merge_runs" value="all"/> - <param name="annotate_indist_groups" value="true"/> - <section name="Merging"> - <param name="annotate_origin" value="false"/> - <param name="allow_disagreeing_settings" value="false"/> - </section> - <section name="Algorithm"> - <param name="min_peptides_per_protein" value="1"/> - <param name="score_aggregation_method" value="maximum"/> - <param name="treat_charge_variants_separately" value="true"/> - <param name="treat_modification_variants_separately" value="true"/> - <param name="use_shared_peptides" value="false"/> - <param name="skip_count_annotation" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinQuantifier"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="median"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="true"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_3_input.featureXML"/> - <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="mean"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="true"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="true"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.idXML"/> - <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinResolver"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="fasta" value="ProteinResolver_1_input.fasta"/> - <param name="in" value="ProteinResolver_1_input.consensusXML"/> - <param name="in_path" value=""/> - <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/> - <section name="resolver"> - <param name="missed_cleavages" value="2"/> - <param name="min_length" value="6"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="designer"> - <param name="experiment" value="ExperimentalSetting"/> - <param name="file" value="File"/> - <param name="separator" value="tab"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PSMFeatureExtractor"> -</xml> - <xml name="autotest_PTModel"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_positive" value="PTModel_1_input_positive.idXML"/> - <param name="in_negative" value="PTModel_1_input_negative.idXML"/> - <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="c" value="0.5"/> - <param name="svm_type" value="C_SVC"/> - <param name="nu" value="0.5"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="max_positive_count" value="1000"/> - <param name="max_negative_count" value="1000"/> - <param name="redundant" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="100.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.1"/> - <param name="nu_step_size" value="1.3"/> - <param name="nu_stop" value="0.9"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_QCCalculator"> -</xml> - <xml name="autotest_QCEmbedder"> -</xml> - <xml name="autotest_QCExporter"> -</xml> - <xml name="autotest_QCExtractor"> -</xml> - <xml name="autotest_QCImporter"> -</xml> - <xml name="autotest_QCMerger"> -</xml> - <xml name="autotest_QCShrinker"> -</xml> - <xml name="autotest_QualityControl"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="QualityControl_1_in.consensusXML"/> - <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/> - <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/> - <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="in_contaminants" value="QualityControl_1.fasta"/> - <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/> - <section name="FragmentMassError"> - <param name="unit" value="auto"/> - <param name="tolerance" value="20.0"/> - </section> - <section name="MS2_id_rate"> - <param name="assume_all_target" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNADigestor"> -</xml> - <xml name="autotest_RNAMassCalculator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_seq" value=""AUCGGC""/> - <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="charge" value="-1 -2"/> - <param name="format" value="list"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNPxlSearch"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value="GUA"/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="false"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value="GUA"/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="true"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="3"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value=""/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="false"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="2"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value=""/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="true"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNPxlXICFilter"> -</xml> - <xml name="autotest_RTEvaluation"> -</xml> - <xml name="autotest_RTModel"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_1_input.idXML"/> - <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.1"/> - <param name="kernel_type" value="POLY"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="total_gradient_time" value="3000.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="10.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.3"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.7"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_positive" value="RTModel_2_input_positive.idXML"/> - <param name="in_negative" value="RTModel_2_input_negative.idXML"/> - <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.5"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="10.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.3"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.7"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_3_input.idXML"/> - <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.001953125"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="1.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="false"/> - <param name="number_of_runs" value="1"/> - <param name="number_of_partitions" value="5"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="0.001953125"/> - <param name="c_step_size" value="2.0"/> - <param name="c_stop" value="0.001953125"/> - <param name="nu_start" value="0.4"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.4"/> - <param name="sigma_start" value="5.0"/> - <param name="sigma_step_size" value="1.221055"/> - <param name="sigma_stop" value="5.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_4_input.txt" ftype="txt"/> - <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.001953125"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="1.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="false"/> - <param name="number_of_runs" value="1"/> - <param name="number_of_partitions" value="5"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="0.001953125"/> - <param name="c_step_size" value="2.0"/> - <param name="c_stop" value="0.001953125"/> - <param name="nu_start" value="0.4"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.4"/> - <param name="sigma_start" value="5.0"/> - <param name="sigma_step_size" value="1.221055"/> - <param name="sigma_stop" value="5.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SeedListGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PepXMLFile_test.mzML"/> - <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="use_peptide_mass" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_1_output.featureXML"/> - <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="use_peptide_mass" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SemanticValidator"> -</xml> - <xml name="autotest_SequenceCoverageCalculator"> -</xml> - <xml name="autotest_SimpleSearchEngine"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SimpleSearchEngine_1.mzML"/> - <param name="database" value="SimpleSearchEngine_1.fasta"/> - <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="Search"> - <param name="enzyme" value="Trypsin"/> - <param name="decoys" value="false"/> - <section name="precursor"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="annotate"> - <param name="PSM" value=""/> - </section> - <section name="peptide"> - <param name="min_size" value="7"/> - <param name="max_size" value="40"/> - <param name="missed_cleavages" value="1"/> - <param name="motif" value=""/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SiriusAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_1_input.mzML"/> - <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_2_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="3"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_3_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="3"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_3_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> - <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_4_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> - <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_4_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_2_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="pubchem"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpecLibCreator"> -</xml> - <xml name="autotest_SpecLibSearcher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpecLibSearcher_1.mzML"/> - <param name="lib" value="SpecLibSearcher_1.MSP"/> - <output_collection name="out" count="1"/> - <param name="compare_function" value="ZhangSimilarityScore"/> - <section name="precursor"> - <param name="mass_tolerance" value="3.0"/> - <param name="mass_tolerance_unit" value="Da"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - </section> - <section name="report"> - <param name="top_hits" value="10"/> - </section> - <section name="filter"> - <param name="remove_peaks_below_threshold" value="2.01"/> - <param name="min_peaks" value="5"/> - <param name="max_peaks" value="150"/> - <param name="cut_peaks_below" value="1000"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraFilterBernNorm"> -</xml> - <xml name="autotest_SpectraFilterMarkerMower"> -</xml> - <xml name="autotest_SpectraFilterNLargest"> -</xml> - <xml name="autotest_SpectraFilterNormalizer"> -</xml> - <xml name="autotest_SpectraFilterParentPeakMower"> -</xml> - <xml name="autotest_SpectraFilterScaler"> -</xml> - <xml name="autotest_SpectraFilterSqrtMower"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraFilterThresholdMower"> -</xml> - <xml name="autotest_SpectraFilterWindowMower"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/> - <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="windowsize" value="50.0"/> - <param name="peakcount" value="2"/> - <param name="movetype" value="slide"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/> - <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="windowsize" value="20.0"/> - <param name="peakcount" value="4"/> - <param name="movetype" value="slide"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraMerger"> -</xml> - <xml name="autotest_SpectraSTSearchAdapter"/> - <xml name="autotest_StaticModification"> -</xml> - <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer"> -</xml> - <xml name="autotest_TargetedFileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="minutes"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="seconds"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> - <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> - <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="traml"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TextExporter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_2_input.consensusXML"/> - <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="RT_then_MZ"/> - <param name="sort_by_maps" value="true"/> - <param name="sort_by_size" value="true"/> - </section> - <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="true"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_5_input.idXML"/> - <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="true"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="true"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_6_input.featureXML"/> - <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_7_input.consensusXML"/> - <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="RT_then_MZ"/> - <param name="sort_by_maps" value="true"/> - <param name="sort_by_size" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_9_input.idXML"/> - <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="0"/> - <param name="add_hit_metavalues" value="0"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TICCalculator"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="regular"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="streaming"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="streaming"/> - <param name="loadData" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="indexed"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="indexed_parallel"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TOFCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TOFCalibration_1_input.mzML"/> - <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> - <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> - <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> - <param name="peak_data" value="false"/> - <section name="algorithm"> - <section name="PeakPicker"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.7"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="400.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.0"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TOFCalibration_2_input.mzML"/> - <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> - <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> - <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> - <param name="peak_data" value="true"/> - <section name="algorithm"> - <section name="PeakPicker"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.7"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="400.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.0"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TransformationEvaluation"> -</xml> - <xml name="autotest_XFDR"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in1.idXML"/> - <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in1.idXML"/> - <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="true"/> - <param name="no_qvalues" value="true"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="0.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-3.0"/> - <param name="maxborder" value="3.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in3.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-3.0"/> - <param name="maxborder" value="3.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in4.idXML"/> - <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="true"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="0.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_XMLValidator"> -</xml> - <xml name="autotest_XTandemAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="all"/> - <param name="max_valid_expect" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="valid"/> - <param name="max_valid_expect" value="1e-14"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteinslong.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="all"/> - <param name="max_valid_expect" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> -<xml name="autotest_InspectAdapter"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_RTPredict"/><xml name="autotest_PTPredict"/><xml name="autotest_IDDecoyProbability"/></macros>
--- a/macros_test.xml Mon Dec 14 16:55:52 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,553 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<macros> - -<!-- a copy of a FileConverter test without the advanced options used - in order to check if this works (all other tests enable advanced) --> -<xml name="manutest_FileConverter"> -<test expect_num_outputs="1"> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> -</test> -</xml> -<!-- tests contributed by the galaxyproteomics community --> -<xml name="manutest_ClusterMassTracesByPrecursor"> - <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/> - </test> -</xml> -<xml name="manutest_ClusterMassTraces"> - <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/> - </test> -</xml> -<xml name="manutest_CVInspector"> - <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 --> - <test expect_num_outputs="1"> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> - <param name="cv_names" value="XLMOD"/> - <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> - <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> - <output name="html" ftype="html" value="CVInspector.html"/> - </test> -</xml> -<xml name="manutest_DeMeanderize"> - <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/> - <output name="out" ftype="mzml" value="DeMeanderize.mzml"/> - </test> -</xml> -<xml name="manutest_Digestor"> - <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="random.fa"/> - <output name="out" ftype="fasta" value="Digestor.fasta"/> - <param name="out_type" value="fasta"/> - </test> -</xml> -<xml name="manutest_EICExtractor"> - <test expect_num_outputs="1"><!-- just using some random test data --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="spectra.mzML"/> - <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> - <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> - </test> -</xml> -<xml name="manutest_ERPairFinder"> - <!-- TODO --> -</xml> -<xml name="manutest_FeatureFinderIsotopeWavelet"> - <test expect_num_outputs="1"><!--just use the input of another FeatureFinder --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> - <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_FFEval"> - <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/> - <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/> - <output name="out" value="FFEval.featureXML" compare="sim_size"/> - <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/> - </test> -</xml> -<xml name="manutest_IDExtractor"> - <test expect_num_outputs="1"><!-- --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> - <param name="best_hits" value="true"/> - <param name="number_of_peptides" value="1"/> - <output name="out" value="IDExtractor.idXML" compare="sim_size"/> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_IDRipper"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_1_input.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> - <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_2_input.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> - <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_output.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> - <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -</xml> -<xml name="manutest_LabeledEval"> - <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> - <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/> - <output name="stdout" value="LabeledEval.txt" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_MapStatistics"> - <test expect_num_outputs="1"><!-- test with a featureXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/> - <output name="out" ftype="txt" value="MapStatistics.txt"/> - </test> - <test expect_num_outputs="1"><!-- test with a consensusxml input --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/> - <output name="out" ftype="txt" value="MapStatistics2.txt"/> - </test> -</xml> -<xml name="manutest_MetaboliteSpectralMatcher"> - <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML --> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="spectra.mzML"/> - <param name="database" value="MetaboliteSpectralDB.mzML"/> - <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/> - </test> -</xml> -<xml name="manutest_MRMPairFinder"> - <!-- TODO no idea about a useful input for pair_in --> -</xml> -<xml name="manutest_MSSimulator"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> - <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> - <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> - </test> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> - <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> - <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> - <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_MzMLSplitter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <param name="parts" value="2"/> - <param name="size" value="0"/> - <param name="unit" value="MB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - <output_collection name="out" type="list" count="2"> - <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/> - <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/> - </output_collection> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <param name="parts" value="1"/> - <param name="size" value="40"/> - <param name="unit" value="KB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - <output_collection name="out" type="list" count="2"> - <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/> - <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/> - </output_collection> -</test> -</xml> -<xml name="manutest_OpenSwathDIAPreScoring"> - <!-- data from a test that included all the needed test files --> - <test> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <output_collection name="output_files" count="1"> - <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - </output_collection> - </test> - - <!-- test with two inputs (actually the same file .. symlinked) --> - <test> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> - <output_collection name="output_files" count="2"> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - </output_collection> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_OpenSwathFileSplitter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> - <output_collection name="outputDirectory" count="6"> - <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> - <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> - </output_collection> - <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> -</xml> -<xml name="manutest_OpenSwathRewriteToFeatureXML"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="adv_opts_cond|test" value="true"/> - <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> - </test> -</xml> -<xml name="manutest_PepNovoAdapter"> - <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection - unclear https://github.com/OpenMS/OpenMS/issues/4719)--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> - <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> - <param name="model" value="LTQ_COMP"/> - </test> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> - <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> - <param name="model" value="LTQ_COMP"/> - </test> -</xml> -<xml name="manutest_PhosphoScoring"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="spectra.mzML"/> - <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> - <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> - </test> -</xml> -<!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 --> -<xml name="manutest_PSMFeatureExtractor"> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> - <param name="multiple_search_engines" value="true"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|skip_db_check" value="true"/> - <param name="out_type" value="idxml"/> - <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/> - </test> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> - <param name="multiple_search_engines" value="true"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|skip_db_check" value="true"/> - <param name="out_type" value="mzid"/> - <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> - </test> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="out_type" value="idxml"/> - <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/> - </test> -</xml> -<xml name="manutest_QCCalculator"> - <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> - <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> - </test> - <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> - <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> - <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> - <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> - </test> - <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> - <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> - <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> - <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> - </test> -</xml> -<xml name="manutest_QCEmbedder"> - <!--TODO--> -</xml> -<xml name="manutest_QCExporter"> - <!--TODO--> -</xml> -<xml name="manutest_QCExtractor"> - <!--TODO--> -</xml> -<xml name="manutest_QCImporter"> - <!--TODO--> -</xml> -<xml name="manutest_QCMerger"> - <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/> - <output name="out" ftype="qcml" value="QCMerger.qcML"/> - </test> -</xml> -<xml name="manutest_QCShrinker"> - <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="qcml" value="QCCalculator1.qcML"/> - <output name="out" ftype="qcml" value="QCShrinker.qcML"/> - </test> -</xml> -<xml name="manutest_RNADigestor"> - <test expect_num_outputs="1"><!--random RNAsequence input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="random_RNA.fa"/> - <output name="out" ftype="fasta" value="RNADigestor.fasta"/> - </test> -</xml> -<xml name="manutest_RNPxlXICFilter"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> - </test> -</xml> -<xml name="manutest_RTEvaluation"> - <!-- just chosen an arbitrary input and autgenerated output--> - <test expect_num_outputs="1"> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/> - <output name="out" ftype="tabular" value="RTEvaluation.tsv"/> - </test> -</xml> -<xml name="manutest_SemanticValidator"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> - <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> - </output> - </test> -</xml> -<xml name="manutest_SequenceCoverageCalculator"> - <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/> - <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/> - <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpecLibCreator"> - <!--TODO could not find test data --> -</xml> -<xml name="manutest_SpectraFilterBernNorm"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterMarkerMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterNLargest"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterNormalizer"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterParentPeakMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterScaler"> - <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterThresholdMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraMerger"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> - <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer"> -<!-- -TODO model_output_file creates multiple files--> -</xml> -<xml name="manutest_TransformationEvaluation"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/> - </test> -</xml> -<xml name="manutest_XMLValidator"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> - </output> - </test> -</xml> -<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
--- a/readme.md Mon Dec 14 16:55:52 2020 +0000 +++ b/readme.md Thu Dec 01 19:05:24 2022 +0000 @@ -74,10 +74,15 @@ Preprocessing: -- For each input / output data set parameter a directory is crated (named by - the parameter) - For input data set parameters the links to the actual location of the data - sets are created + sets are created, the link names are `element_identifier`.`EXT`, where `EXT` + is an extension that is known by OpenMS +- In order to avoid name collisions for the created links each is placed in a + unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name + of the parameter and `DATASET_ID` is the id of the Galaxy dataset +- the same happens for output parameters that are in 1:1 correspondence with + an input parameter + Main:
--- a/test-data.sh Mon Dec 14 16:55:52 2020 +0000 +++ b/test-data.sh Thu Dec 01 19:05:24 2022 +0000 @@ -1,22 +1,25 @@ #!/usr/bin/env bash -VERSION=2.6 -FILETYPES="filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" +VERSION=2.8 +FILETYPES="aux/filetypes.txt" +CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2" # import the magic . ./generate-foo.sh # install conda if [ -z "$tmp" ]; then - tmp=$(mktemp -d) - created="yes" + tmp=$(mktemp -d) + created="yes" fi export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" -export OPENMSENV="$tmp/OpenMS$VERSION-env" -export CTDCONVERTER="$tmp/CTDConverter" +export OPENMSENV="OpenMS$VERSION-env" + +if [ -z "$CTDCONVERTER" ]; then + export CTDCONVERTER="$tmp/CTDConverter" +fi if [[ -z "$1" ]]; then autotests="/dev/null" @@ -25,11 +28,11 @@ fi if type conda > /dev/null; then - true + true else - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh - bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" - source "$tmp/miniconda/bin/activate" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh + bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" + source "$tmp/miniconda/bin/activate" fi eval "$(conda shell.bash hook)" @@ -42,24 +45,27 @@ echo "Clone OpenMS $VERSION sources" if [[ ! -d $OPENMSGIT ]]; then - git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT - cd $OPENMSGIT - git submodule init - git submodule update - cd - + # TODO >2.8 reenable original release branch .. also in else branch + # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917 + # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT + git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT + cd $OPENMSGIT + git submodule init + git submodule update + cd - else - cd $OPENMSGIT - git pull origin release/$VERSION.0 - cd - + cd $OPENMSGIT + git pull origin release/$VERSION.0-plus + cd - fi echo "Create OpenMS $VERSION conda env" # TODO currently add lxml (needed by CTDConverter) # TODO for some reason a to recent openjdk is used if conda env list | grep "$OPENMSENV"; then - true + true else - conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml + conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -69,10 +75,10 @@ echo "Download OpenMS $VERSION package $CONDAPKG" if [[ ! -d $OPENMSPKG ]]; then - mkdir $OPENMSPKG - wget -q -P $OPENMSPKG/ "$CONDAPKG" - tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ - rm $OPENMSPKG/"$(basename $CONDAPKG)" + mkdir $OPENMSPKG + wget -q -P $OPENMSPKG/ "$CONDAPKG" + tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ + rm $OPENMSPKG/"$(basename $CONDAPKG)" fi ############################################################################### @@ -81,40 +87,46 @@ ############################################################################### echo "Clone CTDConverter" if [[ ! -d $CTDCONVERTER ]]; then - #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter - git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER + #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter + git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER else - cd $CTDCONVERTER - git pull origin topic/cdata - cd - + cd $CTDCONVERTER + git pull origin topic/fix-selects2 + cd - fi +conda activate $OPENMSENV +cd $CTDCONVERTER +python -m pip install . --no-deps +cd - +conda deactivate -############################################################################### -## copy all the test data files to test-data -## most of it (outputs) will be overwritten later, but its needed for -## prepare_test_data -############################################################################### + +# ############################################################################### +# ## copy all the test data files to test-data +# ## most of it (outputs) will be overwritten later, but its needed for +# ## prepare_test_data +# ############################################################################### echo "Get test data" -find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ -if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then - wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML - mv MetaboliteSpectralDB.mzML test-data/ +if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then + wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + mv MetaboliteSpectralDB.mzML test-data/ fi ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv if [ ! -d test-data/pepnovo_models/ ]; then - mkdir -p /tmp/pepnovo - wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip - unzip PepNovo.20120423.zip -d /tmp/pepnovo/ - mv /tmp/pepnovo/Models test-data/pepnovo_models/ - rm PepNovo.20120423.zip - rm -rf /tmp/pepnovo + mkdir -p /tmp/pepnovo + wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip + unzip PepNovo.20120423.zip -d /tmp/pepnovo/ + mv /tmp/pepnovo/Models test-data/pepnovo_models/ + rm PepNovo.20120423.zip + rm -rf /tmp/pepnovo fi ############################################################################### ## generate ctd files using the binaries in the conda package @@ -124,17 +136,13 @@ rm -rf ctd mkdir -p ctd -# TODO because of https://github.com/OpenMS/OpenMS/issues/4641 -# this needs to be done from within test-data -cd test-data for i in $OPENMSPKG/bin/* do - b=$(basename $i) - echo $b - $b -write_ctd ../ctd/ - sed -i -e 's/²/^2/' ../ctd/$b.ctd + b=$(basename $i) + echo $b + $b -write_ctd ctd/ + sed -i -e 's/²/^2/' ctd/$b.ctd done -cd - ############################################################################### ## fix ini files: OpenMS test data contains ini files with outdated ini files. ## e.g. variables might be in different nodes, outdated variables present, new @@ -146,17 +154,17 @@ echo "Update test INI files" for ini in test-data/*ini do - tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') - bin=$(which $tool) - if [[ -z $bin ]]; then + tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') + bin=$(which $tool) + if [[ -z $bin ]]; then >&2 echo "missing binary to convert $ini" - continue - fi - cp $ini $ini.backup - $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr - if [[ "$?" -ne "0" ]]; then - >&2 echo "could not convert $ini" - fi + continue + fi + cp $ini $ini.backup + $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr + if [[ "$?" -ne "0" ]]; then + >&2 echo "could not convert $ini" + fi done ############################################################################### @@ -185,17 +193,17 @@ prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh -# prepare_test_data > tmp_test_data.sh -# # remove calls not needed for the tools listed in any .list file -# echo LIST $LIST -# if [ ! -z "$LIST" ]; then -# REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') -# else -# REX=".*" -# fi -# echo REX $REX -# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh -# rm tmp_test_data.sh +## prepare_test_data > tmp_test_data.sh +## # remove calls not needed for the tools listed in any .list file +## echo LIST $LIST +## if [ ! -z "$LIST" ]; then +## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') +## else +## REX=".*" +## fi +## echo REX $REX +## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh +## rm tmp_test_data.sh echo "Execute test shell script" chmod u+x prepare_test_data.sh @@ -204,14 +212,13 @@ cd - || exit -############################################################################### -## create/update test data for the manually generated tests -## - run convert once with the manual tests only and -## - update test-data (needs to run 2x) -############################################################################### +# ############################################################################### +# ## create/update test data for the manually generated tests +# ## - run convert once with the manual tests only and +# ## - update test-data (needs to run 2x) +# ############################################################################### echo "Execute test shell script for manually curated tests" chmod u+x prepare_test_data_manual.sh - cd ./test-data || exit ../prepare_test_data_manual.sh cd - || exit @@ -220,22 +227,28 @@ ############################################################################### ## auto generate tests ############################################################################### + echo "Write test macros to $autotests" echo "<macros>" > "$autotests" -for i in $(ls *xml |grep -v macros) + +for i in $(ls ctd/*ctd) do - b=$(basename "$i" .xml) - get_tests2 "$b" >> "$autotests" + b=$(basename "$i" .ctd) + get_tests2 "$b" >> "$autotests" done echo "</macros>" >> "$autotests" -echo "Create test data links" -link_tmp_files +# echo "Create test data links" +# Breaks DecoyDatabase +# link_tmp_files # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests -# -> OpenSwathFileSplitter IDRipper MzMLSplitter +# -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator +# TODO reevaluate in >2.8 +# - https://github.com/OpenMS/OpenMS/pull/5873 +# - https://github.com/OpenMS/OpenMS/pull/5912 # # Furthermore we remove tests for tools without binaries in conda # -> MSFragger MaRaClusterAdapter NovorAdapter @@ -243,23 +256,23 @@ # not able to specify composite test data # -> SpectraSTSearchAdapter if [[ ! -z "$1" ]]; then - echo "" > macros_discarded_auto.xml - for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter - do - echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml - xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml - echo "</xml>" >> macros_discarded_auto.xml - xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp - mv tmp macros_autotest.xml - done - >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" + echo "" > macros_discarded_auto.xml + for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter + do + echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml + xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml + echo "</xml>" >> macros_discarded_auto.xml + xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp + mv tmp macros_autotest.xml + done + >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" fi conda deactivate ## remove broken symlinks in test-data find test-data/ -xtype l -delete -# if [ ! -z "$created" ]; then -# echo "Removing temporary directory" -# rm -rf "$tmp" -# fi +if [ ! -z "$created" ]; then + echo "Removing temporary directory" + rm -rf "$tmp" +fi
--- a/test-data/spectrast.log Mon Dec 14 16:55:52 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML -GENERAL: File offset size is 8 bytes. Big library supported. -GENERAL: Pointer size is 8 bytes. -MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z -MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; -PERFORMANCE: Total Run Time = 0 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0 seconds.. - -END: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML -========== -START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML -GENERAL: File offset size is 8 bytes. Big library supported. -GENERAL: Pointer size is 8 bytes. -MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z -MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) -SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; -PERFORMANCE: Total Run Time = 1 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0.333333 seconds.. - -END: (Sun Dec 13 17:22:44 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML -==========