annotate MSFraggerAdapter.xml @ 3:3fe401ded316 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"

<?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@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Peptide Identification with MSFragger</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"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&
#if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir opt_out &&
#end if
mkdir database &&
ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("idxml")}'
#if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -opt_out
  'opt_out/output.${gxy2omsext("pepxml")}'
#end if
-database
'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
#if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'opt_out/output.${gxy2omsext("pepxml")}' '$opt_out'
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <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)"/>
    <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="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </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="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </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="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </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">
        <option value="0" selected="true">0</option>
        <option value="1">1</option>
        <option value="2">2</option>
        <expand macro="list_string_san"/>
      </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>
        <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="Lys-C">Lys-C</option>
        <option value="Lys-N">Lys-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="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="Trypsin" selected="true">Trypsin</option>
        <expand macro="list_string_san"/>
      </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"/>
      </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"/>
      </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="">
        <option value="non-enzymatic">non-enzymatic</option>
        <option value="semi">semi</option>
        <option value="fully" selected="true">fully</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="false" 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"/>
      </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=""/>
      <param name="mass_range_min" argument="-digest:mass_range_min" type="float" optional="true" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/>
      <param name="mass_range_max" argument="-digest:mass_range_max" type="float" optional="true" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/>
    </section>
    <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"/>
      </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"/>
      </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="">
        <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"/>
      </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>
    <section name="spectrum" title="Spectrum Processing Parameters" help="" expanded="false">
      <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" optional="true" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/>
      <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" optional="true" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/>
      <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="">
        <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"/>
      </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)"/>
      <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" optional="true" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
    </section>
    <section name="search" title="Open Search Features" help="" expanded="false">
      <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" optional="true" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/>
      <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" optional="true" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/>
      <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" optional="true" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/>
      <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" optional="true" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/>
      <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" optional="true" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/>
      <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=""/>
    </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=""/>
      <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/>
      <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/>
      <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/>
      <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/>
      <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/>
      <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to serine" help=""/>
      <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to proline" help=""/>
      <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to valine" help=""/>
      <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/>
      <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" optional="true" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/>
      <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/>
      <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/>
      <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/>
      <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/>
      <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/>
      <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/>
      <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/>
      <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/>
      <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/>
      <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/>
      <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=""/>
    </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>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="opt_out_FLAG">opt_out (MSFragger optional output file)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
    <data name="opt_out" label="${tool.name} on ${on_string}: opt_out" format="pepxml">
      <filter>OPTIONAL_OUTPUTS is not None and "opt_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <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>
  <help><![CDATA[Peptide Identification with MSFragger


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSFraggerAdapter.html]]></help>
  <expand macro="references"/>
</tool>