Mercurial > repos > bgruening > openms
diff IDFileConverter.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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--- a/IDFileConverter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDFileConverter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,58 +1,110 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="IDFileConverter" name="IDFileConverter" version="1.12.0"> - <description>Converts identification engine file formats.</description> - <macros> - <token name="@EXECUTABLE@">IDFileConverter</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>IDFileConverter +<?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 CTD2Galaxy.--> + <!--Proposed Tool Section: [ID Processing]--> + <tool id="IDFileConverter" name="IDFileConverter" version="2.0.0"> + <description>Converts identification engine file formats.</description> + <macros> + <token name="@EXECUTABLE@">IDFileConverter</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>IDFileConverter --in ${param_in} --out ${param_out} --out_type ${param_out_type} --mz_file ${param_mz_file} --mz_name ${param_mz_name} -${param_use_precursor_data} -${param_peptideprophet_analyzed} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +#if $param_mz_file: + -mz_file $param_mz_file +#end if +#if $param_mz_name: + -mz_name "$param_mz_name" +#end if +#if $param_use_precursor_data: + -use_precursor_data +#end if +#if $param_peptideprophet_analyzed: + -peptideprophet_analyzed +#end if +#if $param_score_type: + -score_type + #if " " in str($param_score_type): + "$param_score_type" + #else + $param_score_type + #end if +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_ignore_proteins_per_peptide} - -scan_regex ${adv_opts.param_scan_regex} + #if $adv_opts.param_ignore_proteins_per_peptide: + -ignore_proteins_per_peptide +#end if + #if $adv_opts.param_scan_regex: + -scan_regex "$adv_opts.param_scan_regex" +#end if + #if $adv_opts.param_count_from_zero: + -count_from_zero +#end if + #if $adv_opts.param_force: + -force +#end if #end if </command> - <inputs> - <param name="param_in" type="data" format="pepXML,idXML" optional="False" label="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#mascotXML: Single Mascot XML file.#br#omssaXML: Single OMSSA XML file.#br#XTandem: Single XML file.#br#idXML: Single idXML file.#br#" help="(-in)"/> - <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content#br#" help="(-out_type)"> - <option value="idXML">idXML</option> - <option value="mzid">mzid</option> - <option value="pepXML">pepXML</option> - <option value="FASTA">FASTA</option> - </param> - <param name="param_mz_file" type="data" format="mzML,mzXML" optional="True" label="[Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in this file" help="(-mz_file)"/> - <param name="param_mz_name" type="text" size="20" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'." help="(-mz_name)"/> - <param name="param_use_precursor_data" type="boolean" truevalue="-use_precursor_data true" falsevalue="-use_precursor_data false" checked="false" optional="True" label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra." help="(-use_precursor_data)"/> - <param name="param_peptideprophet_analyzed" type="boolean" truevalue="-peptideprophet_analyzed true" falsevalue="-peptideprophet_analyzed false" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results." help="(-peptideprophet_analyzed)"/> - <expand macro="advanced_options"> - <param name="param_ignore_proteins_per_peptide" type="boolean" truevalue="-ignore_proteins_per_peptide true" falsevalue="-ignore_proteins_per_peptide false" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain e.g. "+1" in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" help="(-ignore_proteins_per_peptide)"/> - <param name="param_scan_regex" type="text" size="20" label="[mascotXML only] Regular expression used to extract the scan number or retention time. See documentation for details." help="(-scan_regex)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="Output file" format="pepXML"> - <change_format> - <when input="param_out_type" value="idXML" format="idXML"/> - </change_format> - </data> - </outputs> - <help>**What it does** - -Converts identification engine file formats. + <inputs> + <param format="tabular,xml,txt,pepxml" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>" label="Input file or directory containing the data to convert" name="param_in" optional="False" type="data"/> + <param help="(-out_type) " label="Output file type (default: determined from file extension)" name="param_out_type" optional="True" type="select"> + <option value="idXML">idXML</option> + <option value="mzid">mzid</option> + <option value="pepXML">pepXML</option> + <option value="FASTA">FASTA</option> + </param> + <param format="xml,mzxml,mzml" help="(-mz_file) " label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" name="param_mz_file" optional="True" type="data"/> + <param help="(-mz_name) Only necessary if different from 'mz_file'" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" name="param_mz_name" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param checked="false" falsevalue="" help="(-use_precursor_data) " label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra" name="param_use_precursor_data" optional="True" truevalue="-use_precursor_data" type="boolean"/> + <param checked="false" falsevalue="" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" name="param_peptideprophet_analyzed" optional="True" truevalue="-peptideprophet_analyzed" type="boolean"/> + <param help="(-score_type) " label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" name="param_score_type" optional="True" type="select" value="qvalue"> + <option value="qvalue">qvalue</option> + <option value="PEP">PEP</option> + <option value="score">score</option> + </param> + <expand macro="advanced_options"> + <param checked="false" falsevalue="" help="(-ignore_proteins_per_peptide) e.g. "+1" in references column, <br>but do not list extra references in subsequent lines (try -debug 3 or 4)" label="[Sequest only] Workaround to deal with .out files that contain" name="param_ignore_proteins_per_peptide" optional="True" truevalue="-ignore_proteins_per_peptide" type="boolean"/> + <param help="(-scan_regex) See documentation for details" label="[Mascot, Percolator only] Regular expression used to extract the scan number or retention time" name="param_scan_regex" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param checked="false" falsevalue="" help="(-count_from_zero) " label="[Percolator only] Scan numbers extracted by 'scan_regex' start counting at zero (default: start at one)" name="param_count_from_zero" optional="True" truevalue="-count_from_zero" type="boolean"/> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + </expand> + </inputs> + <outputs> + <data format="xml" name="param_out"/> + </outputs> + <help>Converts identification engine file formats. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help> + </tool>