Mercurial > repos > galaxyp > openms_peptideindexer
diff PeptideIndexer.xml @ 9:c4a73c6a8dca draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 03 Sep 2020 16:23:00 +0000 |
| parents | 96dcf92f992d |
| children | cb18120926b0 |
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--- a/PeptideIndexer.xml Fri May 17 10:07:01 2019 -0400 +++ b/PeptideIndexer.xml Thu Sep 03 16:23:00 2020 +0000 @@ -1,164 +1,140 @@ <?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: [ID Processing]--> -<tool id="PeptideIndexer" name="PeptideIndexer" version="2.3.0"> +<tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Refreshes the protein references for all peptide hits.</description> <macros> <token name="@EXECUTABLE@">PeptideIndexer</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[PeptideIndexer + <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($in.ext)' && +mkdir fasta && +ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && +mkdir out && + +## Main program call -#if $param_in: - -in $param_in -#end if -#if $param_fasta: - -fasta $param_fasta -#end if -#if $param_out: - -out $param_out -#end if -#if $param_decoy_string: - -decoy_string "$param_decoy_string" -#end if -#if $param_decoy_string_position: - -decoy_string_position - #if " " in str($param_decoy_string_position): - "$param_decoy_string_position" - #else - $param_decoy_string_position - #end if -#end if -#if $param_missing_decoy_action: - -missing_decoy_action - #if " " in str($param_missing_decoy_action): - "$param_missing_decoy_action" - #else - $param_missing_decoy_action - #end if -#end if -#if $param_write_protein_sequence: - -write_protein_sequence -#end if -#if $param_write_protein_description: - -write_protein_description -#end if -#if $param_keep_unreferenced_proteins: - -keep_unreferenced_proteins -#end if -#if $param_allow_unmatched: - -allow_unmatched -#end if -#if $param_full_tolerant_search: - -full_tolerant_search -#end if -#if $param_aaa_max: - -aaa_max $param_aaa_max -#end if -#if $param_mismatches_max: - -mismatches_max $param_mismatches_max -#end if -#if $param_IL_equivalent: - -IL_equivalent -#end if -#if $param_filter_aaa_proteins: - -filter_aaa_proteins -#end if -#if $param_enzyme_name: - -enzyme:name - #if " " in str($param_enzyme_name): - "$param_enzyme_name" - #else - $param_enzyme_name - #end if -#end if -#if $param_enzyme_specificity: - -enzyme:specificity - #if " " in str($param_enzyme_specificity): - "$param_enzyme_specificity" - #else - $param_enzyme_specificity - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if --threads "\${GALAXY_SLOTS:-1}" -]]></command> +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-fasta +'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' +-out +'out/output.${gxy2omsext("idxml")}' + +## Postprocessing +&& mv 'out/output.${gxy2omsext("idxml")}' '$out' +#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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/> - <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/> - <param name="param_decoy_string" type="text" size="30" value="DECOY_" 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="(-decoy_string) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/> + <param name="fasta" argument="-fasta" type="data" format="fasta" optional="false" label="Input sequence database in FASTA format" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> + <param name="decoy_string" argument="-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"/> </param> - <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) "> + <param name="decoy_string_position" argument="-decoy_string_position" display="radio" type="select" optional="false" 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"/> </param> - <param name="param_missing_decoy_action" display="radio" type="select" optional="False" value="error" 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)" help="(-missing_decoy_action) "> + <param name="missing_decoy_action" argument="-missing_decoy_action" display="radio" type="select" optional="false" 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" selected="true">error</option> <option value="warn">warn</option> + <option value="silent">silent</option> + <expand macro="list_string_san"/> </param> - <param name="param_write_protein_sequence" display="radio" type="boolean" truevalue="-write_protein_sequence" falsevalue="" checked="false" optional="True" label="If set, the protein sequences are stored as well" help="(-write_protein_sequence) "/> - <param name="param_write_protein_description" display="radio" type="boolean" truevalue="-write_protein_description" falsevalue="" checked="false" optional="True" label="If set, the protein description is stored as well" help="(-write_protein_description) "/> - <param name="param_keep_unreferenced_proteins" display="radio" type="boolean" truevalue="-keep_unreferenced_proteins" falsevalue="" checked="false" optional="True" label="If set, protein hits which are not referenced by any peptide are kept" help="(-keep_unreferenced_proteins) "/> - <param name="param_allow_unmatched" display="radio" type="boolean" truevalue="-allow_unmatched" falsevalue="" checked="false" optional="True" label="If set, unmatched peptide sequences are allowed" help="(-allow_unmatched) By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides"/> - <param name="param_full_tolerant_search" display="radio" type="boolean" truevalue="-full_tolerant_search" falsevalue="" checked="false" optional="True" label="If set, all peptide sequences are matched using tolerant search" help="(-full_tolerant_search) Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!"/> - <param name="param_aaa_max" type="integer" min="0" optional="True" value="4" label="[tolerant search only] Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="(-aaa_max) AAAs are 'B', 'Z' and 'X'"/> - <param name="param_mismatches_max" type="integer" min="0" optional="True" value="0" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like"/> - <param name="param_IL_equivalent" display="radio" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/> - <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/> - <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)"> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="TrypChymo">TrypChymo</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Trypsin/P">Trypsin/P</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="V8-DE">V8-DE</option> - <option value="V8-E">V8-E</option> - <option value="PepsinA">PepsinA</option> - <option value="Asp-N">Asp-N</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="Lys-N">Lys-N</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="CNBr">CNBr</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="Lys-C">Lys-C</option> - <option value="Trypsin" selected="true">Trypsin</option> - <option value="Arg-C">Arg-C</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="no cleavage">no cleavage</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <param name="write_protein_sequence" argument="-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="-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="-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="allow_unmatched" argument="-allow_unmatched" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, unmatched peptide sequences are allowed" help="By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides"/> + <param name="aaa_max" argument="-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="-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="-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 occurences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> + <section name="enzyme" title="" help="" expanded="false"> + <param name="name" argument="-enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)"> + <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="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="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="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="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="Trypsin" selected="true">Trypsin</option> + <expand macro="list_string_san"/> + </param> + <param name="specificity" argument="-enzyme:specificity" display="radio" type="select" optional="false" label="Specificity of the enzyme" help="'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. Therefore, the enzyme chosen does not play a role here"> + <option value="full" selected="true">full</option> + <option value="semi">semi</option> + <option value="none">none</option> + <expand macro="list_string_san"/> + </param> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) <br> 'full': both internal cleavage sites must match. <br> 'semi': one of two internal cleavage sites must match. <br> 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here"> - <option value="full" selected="true">full</option> - <option value="semi">semi</option> - <option value="none">none</option> - </param> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - </expand> </inputs> <outputs> - <data name="param_out" format="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Refreshes the protein references for all peptide hits. + <tests> + <expand macro="autotest_PeptideIndexer"/> + <expand macro="manutest_PeptideIndexer"/> + </tests> + <help><![CDATA[Refreshes the protein references for all peptide hits. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeptideIndexer.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_PeptideIndexer.html]]></help> + <expand macro="references"/> </tool>