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annotate spectrast_import.xml @ 0:4e23dcad9087 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
author jjohnson
date Mon, 14 May 2018 14:48:42 -0400
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4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
jjohnson
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1 <tool id="spectrast_import" name="SpectraST Import" version="@VERSION@.0">
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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2 <description>Spectral Library</description>
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3 <macros>
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jjohnson
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4 <import>macros.xml</import>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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5 </macros>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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6 <expand macro="requirements" />
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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7 <command detect_errors="exit_code"><![CDATA[
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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8 ## Symlink dataset to name with recognized ext
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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9 #import re
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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10 #set $ext = '.' + str($input.extension)
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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11 #set $input_name = $re.sub('[.](ms2|msp|hlf)$','',$input.display_name.split('/')[-1]) + $ext
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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12 ln -s '$input' '$input_name' &&
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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13 mkdir -p '$output.files_path' &&
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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14 spectrast -cN'${output.files_path}/library' '$input_name' | tee '$output'
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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15 ]]></command>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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16 <inputs>
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17 <param name="input" type="data" format="ms2,msp,hlf" label="Spectral library ms2, msp, or hlf"
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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18 help="BiblioSpec .ms2, NIST .msp, or X!Hunter .hlf"/>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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19 </inputs>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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20 <outputs>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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21 <data name="output" format="splib"/>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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22 </outputs>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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23 <tests>
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24 <test>
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25 <param name="input" ftype="ms2" value="test.ms2"/>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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26 <output name="output">
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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27 <assert_contents>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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28 <has_text_matching expression="Total number of spectra in library: 1" />
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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29 </assert_contents>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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30 </output>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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31 </test>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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32 </tests>
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33 <help><![CDATA[
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34 **What it does**
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35
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36 Imports a spectral library from the following formats:
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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37
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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38 NIST (National Institute of Standards and Technology)'s .msp format
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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39 X!Hunter's .hlf format
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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40 BiblioSpec's .ms2 format
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41
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42 ]]></help>
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43 <expand macro="citations" />
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44 </tool>