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comparison maxquant.xml @ 18:163452d1e255 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9d6014f26ea5d3737320ec56749207e6fe602025
author galaxyp
date Sun, 13 Nov 2022 19:11:10 +0000
parents 1f39c833f65f
children 8934bc76bb52
comparison
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17:1f39c833f65f 18:163452d1e255
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter> 5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data> 6 </data>
13 <import>macros.xml</import> 13 <import>macros.xml</import>
14 </macros> 14 </macros>
15 <expand macro="requirements"/> 15 <expand macro="requirements"/>
16 <expand macro="required_files"/> 16 <expand macro="required_files"/>
17 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
18 ## this is needed to avoid dotnet from crashing, in a newer dotnet version we can remove that
19 export COMPlus_EnableDiagnostics=0 &&
18 #import re 20 #import re
19 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr 21 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr
20 22
21 ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0) 23 ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0)
22 ## Should be removed as soon as MQ is updated with a fixed version 24 ## Should be removed as soon as MQ is updated with a fixed version