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comparison macros.xml @ 51:66690eb50a32 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1165d86d2f2714093577c54b7e6d3a7149778bd3
author galaxyp
date Mon, 31 Dec 2018 02:20:36 -0500
parents 5814883aa217
children 864bd76db767
comparison
equal deleted inserted replaced
50:5814883aa217 51:66690eb50a32
10 <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"/>
11 <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/> 11 <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
12 <regex match="CompomicsError" level="fatal" description="Compomics Error"/> 12 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
13 </stdio> 13 </stdio>
14 </xml> 14 </xml>
15
15 <token name="@GENERAL_PARAMETERS@"> 16 <token name="@GENERAL_PARAMETERS@">
16 -frag_tol '${precursor_options.fragment_tol}' 17 -frag_tol '${precursor_options.fragment_tol}'
17 -frag_ppm '${precursor_options.fragment_tol_units}' 18 -frag_ppm '${precursor_options.fragment_tol_units}'
18 -prec_tol '${precursor_options.precursor_ion_tol}' 19 -prec_tol '${precursor_options.precursor_ion_tol}'
19 -prec_ppm '${precursor_options.precursor_ion_tol_units}' 20 -prec_ppm '${precursor_options.precursor_ion_tol_units}'
51 #if $variable_mods_str 52 #if $variable_mods_str
52 -variable_mods "$variable_mods_str" 53 -variable_mods "$variable_mods_str"
53 #end if 54 #end if
54 55
55 </token> 56 </token>
57
56 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> 58 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
57 <token name="@SEARCHGUI_VERSION@">3.3.6</token> 59 <token name="@SEARCHGUI_VERSION@">3.3.10</token>
58 <token name="@PEPTIDESHAKER_VERSION@">1.16.32</token> 60 <token name="@PEPTIDESHAKER_VERSION@">1.16.36</token>
59 <xml name="general_options"> 61 <xml name="general_options">
60 62
61 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> 63 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
62 <conditional name="digestion"> 64 <conditional name="digestion">
63 <param name="cleavage" type="select" label="Digestion"> 65 <param name="cleavage" type="select" label="Digestion">