Mercurial > repos > galaxyp > encyclopedia_prosit_csv_to_library

annotate encyclopedia_prosit_csv_to_library.xml @ 1:0e25453fbee7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 64740168b7816f0fe38f6f0629cb7e618cd42878"
author galaxyp
date Thu, 08 Apr 2021 17:54:59 +0000
parents 8a9cef108b0c
children 2aad7301632d
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0e25453fbee7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 64740168b7816f0fe38f6f0629cb7e618cd42878"
galaxyp
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1 <tool id="encyclopedia_prosit_csv_to_library" name="ConvertPrositCSVToLibrary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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2 <description>Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library</description>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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3 <macros>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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4 <import>macros.xml</import>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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5 </macros>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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6 <expand macro="requirements" />
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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7 <command detect_errors="aggressive"><![CDATA[
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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8 EncyclopeDIA -convert -prositcsvtolibrary
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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9 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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10 -i '$i'
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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11 -f '$f'
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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12 -o '$output'
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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13 #if $istest == 'yes'
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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14 && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output'
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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15 #end if
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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16 ]]></command>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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17 <inputs>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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18 <param argument="-i" type="data" format="csv" label="Prosit output csv file"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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19 <param argument="-f" type="data" format="fasta" label="Protein Fasta database"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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20 <param name="istest" type="hidden" value="no"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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21 </inputs>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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22 <outputs>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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23 <data name="output" format="dlib" label="${i.name} DLIB"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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24 <data name="test_output" format="txt" >
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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25 <filter>istest == 'yes'</filter>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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26 </data>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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27 </outputs>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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28 <tests>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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29 <test>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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30 <param name="i" ftype="csv" value="PrositLib.csv"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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31 <param name="f" ftype="fasta" value="YeastProteinFasta5.fasta"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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32 <param name="istest" value="yes"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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33 <output name="test_output" ftype="txt">
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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34 <assert_contents>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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35 <has_text text="PCL1_YEAST"/>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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36 </assert_contents>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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37 </output>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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38 </test>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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39 </tests>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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40 <help><![CDATA[
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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41 Convert Prosit/Spectronaut CSV to library DLIB
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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42 ]]></help>
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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43 <expand macro="citations" />
8a9cef108b0c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
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44 </tool>