Mercurial > repos > galaxyp > encyclopedia_prosit_csv_to_library

comparison encyclopedia_prosit_csv_to_library.xml @ 1:c0a3bd187e2b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
author galaxyp
date Mon, 14 Sep 2020 16:58:50 +0000
parents 4402e78f068d
children 76133c933d92
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0:4402e78f068d 1:c0a3bd187e2b
2 <description>Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library</description> 2 <description>Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 EncyclopeDIA -convert -prositcsvtolibrary 8 EncyclopeDIA -convert -prositcsvtolibrary
9 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
9 -i '$i' 10 -i '$i'
10 -f '$f' 11 -f '$f'
11 -o '$output' 12 -o '$output'
12 #if $istest == 'yes' 13 #if $istest == 'yes'
13 && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output' 14 && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output'
14 #end if 15 #end if
15 ]]></command> 16 ]]></command>
16 <inputs> 17 <inputs>