Mercurial > repos > jjohnson > encyclopedia_prosit_csv_to_library
comparison encyclopedia_prosit_csv_to_library.xml @ 0:75d11473e378 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author | jjohnson |
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date | Fri, 19 Jun 2020 10:20:35 -0400 |
parents | |
children | 602d01de42b4 |
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-1:000000000000 | 0:75d11473e378 |
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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="exit_code"><![CDATA[ | |
8 EncyclopeDIA -convert -prositcsvtolibrary | |
9 -i '$i' | |
10 -f '$f' | |
11 -o '$output' | |
12 #if $istest == 'yes' | |
13 && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output' | |
14 #end if | |
15 ]]></command> | |
16 <inputs> | |
17 <param argument="-i" type="data" format="csv" label="Prosit output csv file"/> | |
18 <param argument="-f" type="data" format="fasta" label="Protein Fasta database"/> | |
19 <param name="istest" type="hidden" value="no"/> | |
20 </inputs> | |
21 <outputs> | |
22 <data name="output" format="dlib" label="${i.name} DLIB"/> | |
23 <data name="test_output" format="txt" > | |
24 <filter>istest == 'yes'</filter> | |
25 </data> | |
26 </outputs> | |
27 <tests> | |
28 <test> | |
29 <param name="i" ftype="csv" value="PrositLib.csv"/> | |
30 <param name="f" ftype="fasta" value="YeastProteinFasta5.fasta"/> | |
31 <param name="istest" value="yes"/> | |
32 <output name="test_output" ftype="txt"> | |
33 <assert_contents> | |
34 <has_text text="PCL1_YEAST"/> | |
35 </assert_contents> | |
36 </output> | |
37 </test> | |
38 </tests> | |
39 <help><![CDATA[ | |
40 Convert Prosit/Spectronaut CSV to library DLIB | |
41 ]]></help> | |
42 <expand macro="citations" /> | |
43 </tool> |