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comparison encyclopedia_prosit_csv_to_library.xml @ 0:75d11473e378 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author jjohnson
date Fri, 19 Jun 2020 10:20:35 -0400
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children 602d01de42b4
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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>