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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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4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
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1 <tool id="spectrast_import" name="SpectraST Import" version="@VERSION@.0">
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274fdc50169b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty
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2 <description>to Spectral Library from ms2, msp, or hlf</description>
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3 <macros>
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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>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## Symlink dataset to name with recognized ext
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9 #import re
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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' '$input_name' &&
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13 mkdir -p libdir &&
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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14 spectrast -cN'libdir/library' '$input_name' | tee '$output' &&
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15 mkdir -p '$output.files_path' &&
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16 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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17 ]]></command>
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18 <inputs>
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19 <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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20 help="BiblioSpec .ms2, NIST .msp, or X!Hunter .hlf"/>
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21 <param name="bin" type="boolean" truevalue="" falsevalue="-c_BIN!" checked="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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22 label="Write library in binary format, which enables quicker search."/>
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="splib"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <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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30 <output name="output">
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31 <assert_contents>
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32 <has_text_matching expression="Total number of spectra in library: 1" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 **What it does**
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39
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40 Imports a spectral library from the following formats:
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41
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42 NIST (National Institute of Standards and Technology)'s .msp format
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43 X!Hunter's .hlf format
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44 BiblioSpec's .ms2 format
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45
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46 ]]></help>
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47 <expand macro="citations" />
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48 </tool>