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annotate spectrast_create.xml @ 0:c8895a92b74d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/protk-galaxytools/tree/master/spectrast commit 34735d62618a252173e3c90436f240659484727a
author galaxyp
date Thu, 29 Mar 2018 09:51:50 -0400
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c8895a92b74d planemo upload for repository https://github.com/galaxyproteomics/protk-galaxytools/tree/master/spectrast commit 34735d62618a252173e3c90436f240659484727a
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1 <tool id="spectrast_create_1" name="SpectraST Create" version="5.0.0">
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2 <description>Create Spectral Libraries</description>
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3 <requirements>
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4 <!--
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5 <container type="docker">iracooke/protk-1.4.3</container>
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6 -->
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7 <requirement type="package" version="1.4.4a">protk</requirement>
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8 <requirement type="package" version="5.0.0">tpp</requirement>
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9 </requirements>
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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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13 <command>
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14 <![CDATA[
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15 spectrast_create.rb --galaxy
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16
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17 #for $pepxml_file in $pepxml_files:
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18 ${pepxml_file}
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19 #end for
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20
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21 --spectrum-files='$spectrum_files'
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22 --predicate 'Protein!~$decoy_prefix_string'
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23 --p-thresh $p_thresh
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24 --instrument-acquisition $instrument_acquisition
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25 -o library
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26
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27 &&
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29 mkdir -p $output.files_path
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30
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31 &&
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32
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33 cp library.splib library.spidx library.pepidx $output.files_path/
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34
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35 &&
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37 echo "Spectral Library Primary File" > $output
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38 ]]>
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39 </command>
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40 <inputs>
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41
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42 <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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44 <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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45 <param name="instrument_acquisition" type="text" value="CID-QTOF" label="Decoy String" size="20"
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46 help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
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47 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra."/>
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48 <param name="p_thresh" type="float" value="0.99" min="0" max="1" label="Probability Threshold"
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49 help="Matches scoring less than this value are discarded" />
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50 </inputs>
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51 <outputs>
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52 <data format="splib" name="output"/>
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53 </outputs>
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54 <help>
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55 <![CDATA[
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56 **What it does**
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57
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58 Create Spectral Libraries.
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59
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60 ]]>
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61 </help>
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62 </tool>