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annotate spectrast_filter.xml @ 12:f6fd2798879a draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:41:43 -0400
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1 <tool id="spectrast_filter_1" name="SpectraST Filter" version="1.0.0">
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2 <description>Filter and Manipulate Spectral Libraries</description>
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.3</container>
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5 <requirement type="package" version="1.4.3">protk</requirement>
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6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Job Failed" />
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10 </stdio>
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11 <command>
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12 <![CDATA[
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13 spectrast_filter.rb --merge $merge
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14
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15 #for $splib_file in $splib_files:
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16 ${splib_file.extra_files_path}/library.splib
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17 #end for
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19 --replicates $replicates
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20 -o library
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21
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22 &&
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24 mkdir -p ${output.files_path}
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25
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26 &&
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28 cp library.splib library.spidx library.pepidx ${output.files_path}/
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30 &&
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32 echo "Spectral Library Primary File" > $output
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
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37 <param name="merge" type="select" format="text">
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38 <label>Merge Method</label>
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39 <option value="U">Union</option>
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40 <option value="S">Subtraction</option>
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41 <option value="H">Subtraction of homologs</option>
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42 <option value="A">Appending</option>
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43 </param>
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45 <param name="replicates" type="select" format="text">
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46 <label>How to deal with replicate spectra</label>
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47 <option value="None">Keep All</option>
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48 <option value="C">Consensus</option>
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49 <option value="B">Best replicate</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data format="splib" name="output"/>
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54 </outputs>
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55 <help>
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56 <![CDATA[
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57 **What it does**
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58
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59 Filter and Manipulate Spectral Libraries
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60
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61 ]]>
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62 </help>
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63 </tool>