Mercurial > repos > galaxyp > rawtools
diff rawtools.xml @ 0:51e4aa55ea04 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
| author | galaxyp |
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| date | Fri, 05 Apr 2019 04:16:26 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rawtools.xml Fri Apr 05 04:16:26 2019 -0400 @@ -0,0 +1,279 @@ +<tool id="rawtools" name="Raw Tools" version="@RAWTOOLS_VERSION@.@TOOL_SUBVERSION@" profile="16.04"> + <description> + Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files. + </description> + <macros> + <token name="@RAWTOOLS_VERSION@">1.4.2</token> + <token name="@TOOL_SUBVERSION@">0</token> + <xml name="input_fasta"> + <param format="fasta" name="input_database" type="data" label="Protein Database" + help="Select FASTA database from history"/> + </xml> + </macros> + <requirements> + <requirement type="package" version="@RAWTOOLS_VERSION@">rawtools</requirement> + </requirements> + <command detect_errors="exit_code"> +<![CDATA[ + #from datetime import datetime + #import json + #import os + #import re + #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $temp_stderr = "rawtools_stderr" + #set $bin_dir = "bin" + + mkdir output && + cwd=`pwd` && + ## TODO: To remove this patch when dropping support for Galaxy 17_09, adding profile="18.01" to the tool. + export HOME=\$cwd && + + mkdir raws_folder && + #for $input_raw in $input_raws: + #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw") + ln -s -f '${input_raw}' './raws_folder/${input_name}' && + #end for + + ##################### + ## Raw Tools ## + ##################### + (rawtools.sh + + ## PARSING AND QUANTIFICATION OPTIONS + + ## If any processing option is enabled in parsing & quantification, "parse" command is mandatory + #if $pq_options.pq_conditional.matrix_select == "yes" or $pq_options.chromatogram_conditional.chromatogram_select == "yes" or $pq_options.mgf_conditional.mgf_select == "yes" or $pq_options.metrics_boolean == "yes": + parse + #end if + --directory ./raws_folder + + ## Generates Matrix file + #if $pq_options.pq_conditional.matrix_select == "yes": + --parse + #end if + + ## Generates quantification information + #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.q_conditional.q_select == "yes" : + --quant + --labelingreagent ${pq_options.pq_conditional.q_conditional.q_labeling_reagent} + #end if + + ## Unlabeled quant + #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.unlabeledquant_boolean == "yes": + --unlabeledquant + #end if + + ## Generates Mgf file + #if $pq_options.mgf_conditional.mgf_select == "yes": + --writemgf + --masscutoff ${pq_options.mgf_conditional.mgf_masscutoff} + ## DEPRECATED --intensitycutoff ${pq_options.mgf_conditional.mgf_intensitycutoff} + #if $pq_options.mgf_conditional.mgf_refinement == "yes": + -R + #end if + #end if + + ## Generates chromatogram file + #if $pq_options.chromatogram_conditional.chromatogram_select == "yes": + --chro ${pq_options.chromatogram_conditional.chromatogram_type}${pq_options.chromatogram_conditional.chromatogram_order} + #end if + + ## Generates metrics file + #if $pq_options.metrics_boolean == "yes": + --metrics + #end if + + --out \$cwd/output + + 2>> $temp_stderr) && + + cat $temp_stderr 2>&1; +]]> + </command> + <inputs> + <param format="thermo.raw" name="input_raws" type="data" label="Raw file" multiple="true" + help="Select the raw file from history"/> + <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses a proprietary vendor library; to run it you must agree to the vendor license. Read it at https://github.com/kevinkovalchik/RawTools/blob/master/RawFileReaderLicense"> + <validator type="expression" message="You must agree to the vendor license to run RawTools.">True == value</validator> + </param> + <section name="pq_options" expanded="true" title="Parsing and Quantification"> + <conditional name="pq_conditional"> + <param name="matrix_select" type="select" + label="Create Matrix file" + help="Parses raw file meta and scan data and creates a tab-delimited text file."> + <option value="yes" selected="True">Yes</option> + <option value="no" >No</option> + </param> + <when value="yes"> + <conditional name="q_conditional"> + <param name="q_select" type="select" + label="Quantification" + help="Also quantifies reporter ions and write results to output matrix."> + <option value="yes" >Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="q_labeling_reagent" label="Labeling reagent" type="select" + help="Reagents used to label peptides."> + <option value="TMT0" selected="True">TMT0</option> + <option value="TMT2" >TMT2</option> + <option value="TMT6" >TMT6</option> + <option value="TMT10" >TMT10</option> + <option value="TMT11" >TMT11</option> + <option value="iTRAQ4" >iTRAQ4</option> + <option value="iTRAQ8" >iTRAQ8</option> + </param> + </when> + <when value="no" /> + </conditional> + <param name="unlabeledquant_boolean" label="Unlabeled quant" type="boolean" truevalue="yes" falsevalue="no" + help="Calculate areas of precursor peaks and writes them to the matrix file as ParentPeakArea column."/> + </when> + <when value="no" /> + </conditional> + + <conditional name="mgf_conditional"> + <param name="mgf_select" type="select" label="Creates a mgf file" + help="Creates a standard MGF file."> + <option value="yes" >Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="mgf_masscutoff" label="Mass cutoff" value="0" type="float" + help="Specify a mass cutoff to be applied when generating MGF files. May be of use if removal of reporter ions is desired prior to searching of MS2 spectra."/> + <!--<param name="mgf_intensitycutoff" label="Intensity cutoff" value="0" type="float" + help="Relative intensity cutoff for ions included in a MGF file. The value is relative to the highest intensity ion found in a given scan."/> + --> + <param name="mgf_refinement" label="Precursor mass and charge refinement" type="boolean" truevalue="yes" falsevalue="no" checked="false" + help="Refine precursor charge and monoisotopic mass assignments. Highly recommended if monoisotopic precursor selection was turned off in the instrument method (or peptide match on a QE instrument)."/> + + </when> + <when value="no" /> + </conditional> + <conditional name="chromatogram_conditional"> + <param name="chromatogram_select" type="select" + label="Create chromatogram" + help="Creates a text file of chromatographic data for investigation or plotting."> + <option value="yes" >Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="chromatogram_type" label="Chromatogram type" type="select" help="MS Level"> + <option value="1" selected="True">MS1</option> + <option value="2" >MS2</option> + <option value="3" >MS3</option> + </param> + <param name="chromatogram_order" label="Chromatogram order" type="select" help="MS Order"> + <option value="T" >TIC</option> + <option value="B" >Base peak</option> + <option value="TB" selected="True">TIC and base peak</option> + </param> + </when> + <when value="no" /> + </conditional> + <param name="metrics_boolean" label="Create metrics" type="boolean" truevalue="yes" falsevalue="no" + help="Creates a text file containing general metrics about the Ms run." /> + + </section> + + <!-- TODO: QUALITY CONTROL + <section name="quality_control_options" expanded="false" title="Quality control"> + + </section> + --> + + </inputs> + <outputs> + <!-- Matrix --> + + <collection name="output_matrix" type="list" label="${tool.name} - ${on_string}: Matrix"> + <filter>pq_options['pq_conditional']['matrix_select'] == "yes"</filter> + <discover_datasets pattern="(?P<designation>.+)\.raw_Matrix.txt" ext="txt" directory="output"/> + </collection> + + <!-- MGF file --> + + <collection name="output_mgf" type="list" label="${tool.name} - ${on_string}: MGF"> + <filter>pq_options['mgf_conditional']['mgf_select'] == "yes"</filter> + <discover_datasets pattern="(?P<designation>.+)\.mgf" ext="mgf" directory="output"/> + </collection> + + <!-- Chromatogram file --> + + <collection name="output_chromatogram" type="list" label="${tool.name} - ${on_string}: Chromatogram" > + <filter>pq_options['chromatogram_conditional']['chromatogram_select'] == "yes"</filter> + <discover_datasets pattern="(?P<designation>.+)\.raw_Ms_BP_chromatogram.txt" ext="txt" directory="output"/> + </collection> + + <!-- Metrics file --> + + <collection name="output_metrics" type="list" label="${tool.name} - ${on_string}: Metrics" > + <filter>pq_options['metrics_boolean'] is True</filter> + <discover_datasets pattern="(?P<designation>.+)\.raw_Metrics.txt" ext="txt" directory="output"/> + </collection> + </outputs> + <tests> + + <!-- Test Matrix --> + <test> + <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/> + <param name="license_agreement" value="true" /> + <param name="pq_conditional|matrix_select" value="yes"/> + <output_collection name="output_matrix" type="list"> + <element name="really_small" file="really_small.raw_Matrix.txt" ftype="txt" compare="sim_size" delta="3000"/> + </output_collection> + </test> + + <!-- Test mgf conversion --> + <test> + <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/> + <param name="license_agreement" value="true" /> + <param name="pq_conditional|matrix_select" value="no"/> + <param name="mgf_conditional|mgf_select" value="yes"/> + <param name="mgf_conditional|mgf_refinement" value="yes"/> + <output_collection name="output_mgf" type="list"> + <element name="really_small.raw" ftype="mgf"> + <assert_contents> + <has_text text="PEPMASS=675.248779296875"/> + <has_text text="RTINSECONDS=73.863181104"/> + <has_text text="SCANS=36"/> + <has_text text="121.31165 920.2368"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- Test chromatogram --> + <test> + <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/> + <param name="license_agreement" value="true" /> + <param name="pq_conditional|matrix_select" value="no"/> + <param name="chromatogram_conditional|chromatogram_select" value="yes"/> + <output_collection name="output_chromatogram" type="list" > + <element name="really_small" file="really_small.raw_Ms_BP_chromatogram.txt" ftype="txt" compare="sim_size" delta="3000"/> + </output_collection> + </test> + + + </tests> + <help> +**What it does** + +RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis (to be developed in further versions) of Thermo Orbitrap raw mass spectrometer files. + +RawTools is written in C# and uses the Thermo RawFileReader library. RawTools is the replacement for RawQuant Python package. + +https://github.com/kevinkovalchik/RawTools + +**License** + +Raw Tools is a free open-source project, following an Apache License 2.0. + +RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved. +Using this software implies the acceptance of RawFileReader license terms. + + </help> + <citations> + <citation type="doi">doi:10.1021/acs.jproteome.8b00721</citation> + </citations> +</tool>