Mercurial > repos > galaxyp > peptideshaker

comparison macros.xml @ 49:58a3e6cb2598 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
author galaxyp
date Fri, 12 Oct 2018 08:56:06 -0400
parents 44ca2967218c
children 5814883aa217
comparison
equal deleted inserted replaced
48:64e3a8cc8ffb 49:58a3e6cb2598
1 <macros> 1 <macros>
2 <xml name="stdio"> 2 <xml name="stdio">
3 <stdio> 3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" /> 4 <exit_code range="1:" level="fatal" description="Job Failed" />
5 <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/> 5 <!-- <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
6 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> 6 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
7 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> 7 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
8 <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>-->
8 <regex match="java.*Exception" level="fatal" description="Java Exception"/> 9 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
9 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 10 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
10 <regex match="CompomicsError" level="fatal" description="Compomics Error"/> 11 <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
12 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
11 </stdio> 13 </stdio>
12 </xml> 14 </xml>
13 <token name="@GENERAL_PARAMETERS@"> 15 <token name="@GENERAL_PARAMETERS@">
14 -frag_tol '${precursor_options.fragment_tol}' 16 -frag_tol '${precursor_options.fragment_tol}'
15 -frag_ppm '${precursor_options.fragment_tol_units}' 17 -frag_ppm '${precursor_options.fragment_tol_units}'
50 -variable_mods "$variable_mods_str" 52 -variable_mods "$variable_mods_str"
51 #end if 53 #end if
52 54
53 </token> 55 </token>
54 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> 56 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
55 <token name="@SEARCHGUI_VERSION@">3.3.3</token> 57 <token name="@SEARCHGUI_VERSION@">3.3.5</token>
58 <token name="@PEPTIDESHAKER_VERSION@">1.16.31</token>
56 <xml name="general_options"> 59 <xml name="general_options">
57 60
58 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> 61 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
59 <conditional name="digestion"> 62 <conditional name="digestion">
60 <param name="cleavage" type="select" label="Digestion"> 63 <param name="cleavage" type="select" label="Digestion">