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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty
author jjohnson
date Wed, 25 Jul 2018 15:05:34 -0400
parents c9bfe6adb7cd
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1 <tool id="spectrast_filter" name="SpectraST Filter" version="@VERSION@.0">
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2 <description>and Manipulate Spectral Libraries</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 python $__tool_directory__/spectrast_params.py
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9 --mode=filter
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10 #if $spectrastParams:
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11 '$spectrastParams'
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12 #end if
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13 '$spectrast_params' -o spectrast_create.params &&
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14 mkdir -p outdir &&
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15 spectrast -cFspectrast_create.params -cN'outdir/library'
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16 #for $splib_file in $splib_files:
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17 ${splib_file.extra_files_path}/library.splib
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18 #end for
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19 &&
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20 mkdir -p '$output.files_path' &&
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21 for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done
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22 ]]>
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23 </command>
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24 <configfiles>
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25 <configfile name="spectrast_params"><![CDATA[#slurp
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26 ]]>
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27 @LIBRARY_CREATE_OPTIONS@
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28 @LIBRARY_MANIPULATION_OPTIONS@
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29 </configfile>
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30 </configfiles>
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31 <inputs>
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32 <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
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33 <param name="spectrastParams" type="data" format="txt" optional="true" label="SpectraST param file" help=""/>
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34 <expand macro="library_create_options"/>
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35 <expand macro="library_manipulation_options"/>
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36 </inputs>
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37 <outputs>
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38 <data name="log" format="txt" label="spectrast.log" from_work_dir="spectrast.log"/>
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39 <data name="params" format="txt" label="spectrast_create.params" from_work_dir="spectrast_create.params"/>
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40 <expand macro="library_create_outputs"/>
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41 <data format="splib" name="output"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 </test>
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46 </tests>
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47 <help>
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48 <![CDATA[
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49 **What it does**
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50
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51 Filter and Manipulate Spectral Libraries
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52
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53 ]]>
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54 </help>
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55 </tool>