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annotate spectrast_create.xml @ 8:276ff5e1732c draft

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Add spectrast_filter tool
author iracooke
date Wed, 20 May 2015 01:35:51 -0400
parents c10b55821212
children f6fd2798879a
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1 <tool id="spectrast_create_1" name="SpectraST Create" version="1.0.0">
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2 <requirements>
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3 <container type="docker">iracooke/protk-1.4.2</container>
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4 <requirement type="package" version="1.4">protk</requirement>
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5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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6 </requirements>
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8 <description>Create Spectral Libraries</description>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Job Failed" />
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12 </stdio>
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14 <command>
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15 spectrast_create.rb --galaxy
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17 #for $pepxml_file in $pepxml_files:
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18 ${pepxml_file}
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19 #end for
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21 --spectrum-files='$spectrum_files'
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23 --predicate 'Protein!~$decoy_prefix_string'
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25 --p-thresh $p_thresh
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27 --instrument-acquisition $instrument_acquisition
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29 -o library;
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31 mkdir -p $output.extra_files_path;
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33 cp library.splib library.spidx library.pepidx $output.extra_files_path/;
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35 echo "Spectral Library Primary File" > $output
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37 </command>
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39 <inputs>
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41 <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
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43 <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>
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45 <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/>
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47 <param name="instrument_acquisition" help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
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48 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra." type="text" value="CID-QTOF" label="Decoy String" size="20"/>
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50 <param name="p_thresh" help="Matches scoring less than this value are discarded" type="float" value="0.99" min="0" max="1" label="Probability Threshold"/>
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52 </inputs>
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54 <outputs>
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55 <data format="splib" name="output"/>
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56 </outputs>
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58 </tool>