Mercurial > repos > galaxyp > spectrast
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planemo upload for repository https://github.com/galaxyproteomics/protk-galaxytools/tree/master/spectrast commit 34735d62618a252173e3c90436f240659484727a
author | galaxyp |
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date | Thu, 29 Mar 2018 09:51:50 -0400 |
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<tool id="spectrast_create_1" name="SpectraST Create" version="5.0.0"> <description>Create Spectral Libraries</description> <requirements> <!-- <container type="docker">iracooke/protk-1.4.3</container> --> <requirement type="package" version="1.4.4a">protk</requirement> <requirement type="package" version="5.0.0">tpp</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> </stdio> <command> <![CDATA[ spectrast_create.rb --galaxy #for $pepxml_file in $pepxml_files: ${pepxml_file} #end for --spectrum-files='$spectrum_files' --predicate 'Protein!~$decoy_prefix_string' --p-thresh $p_thresh --instrument-acquisition $instrument_acquisition -o library && mkdir -p $output.files_path && cp library.splib library.spidx library.pepidx $output.files_path/ && echo "Spectral Library Primary File" > $output ]]> </command> <inputs> <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/> <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/> <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/> <param name="instrument_acquisition" type="text" value="CID-QTOF" label="Decoy String" size="20" help="Set the instrument and acquisition settings of the spectra (in case not specified in data files). Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra."/> <param name="p_thresh" type="float" value="0.99" min="0" max="1" label="Probability Threshold" help="Matches scoring less than this value are discarded" /> </inputs> <outputs> <data format="splib" name="output"/> </outputs> <help> <![CDATA[ **What it does** Create Spectral Libraries. ]]> </help> </tool>