Mercurial > repos > galaxyp > encyclopedia_prosit_csv_to_library
comparison encyclopedia_prosit_csv_to_library.xml @ 0:8a9cef108b0c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
| author | galaxyp |
|---|---|
| date | Mon, 14 Sep 2020 17:06:37 +0000 |
| parents | |
| children | 0e25453fbee7 |
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| -1:000000000000 | 0:8a9cef108b0c |
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| 1 <tool id="encyclopedia_prosit_csv_to_library" name="ConvertPrositCSVToLibrary" version="@VERSION@.0" python_template_version="3.5"> | |
| 2 <description>Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 EncyclopeDIA -convert -prositcsvtolibrary | |
| 9 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}" | |
| 10 -i '$i' | |
| 11 -f '$f' | |
| 12 -o '$output' | |
| 13 #if $istest == 'yes' | |
| 14 && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output' | |
| 15 #end if | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param argument="-i" type="data" format="csv" label="Prosit output csv file"/> | |
| 19 <param argument="-f" type="data" format="fasta" label="Protein Fasta database"/> | |
| 20 <param name="istest" type="hidden" value="no"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="output" format="dlib" label="${i.name} DLIB"/> | |
| 24 <data name="test_output" format="txt" > | |
| 25 <filter>istest == 'yes'</filter> | |
| 26 </data> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="i" ftype="csv" value="PrositLib.csv"/> | |
| 31 <param name="f" ftype="fasta" value="YeastProteinFasta5.fasta"/> | |
| 32 <param name="istest" value="yes"/> | |
| 33 <output name="test_output" ftype="txt"> | |
| 34 <assert_contents> | |
| 35 <has_text text="PCL1_YEAST"/> | |
| 36 </assert_contents> | |
| 37 </output> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help><![CDATA[ | |
| 41 Convert Prosit/Spectronaut CSV to library DLIB | |
| 42 ]]></help> | |
| 43 <expand macro="citations" /> | |
| 44 </tool> |