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comparison macros.xml @ 30:ad60446b1e93 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
author galaxyp
date Fri, 13 Jan 2017 14:15:42 -0500
parents 78fad25eff17
children ff592231f118
comparison
equal deleted inserted replaced
29:78fad25eff17 30:ad60446b1e93
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.*Exception" level="fatal" description="Java Exception"/> 5 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
7 </stdio> 8 </stdio>
8 </xml> 9 </xml>
9 <token name="@GENERAL_PARAMETERS@"> 10 <token name="@GENERAL_PARAMETERS@">
10 -frag_tol "${fragment_tol}" 11 -frag_tol "${fragment_tol}"
12 ### -frag_ppm
11 -prec_tol "${precursor_ion_tol}" 13 -prec_tol "${precursor_ion_tol}"
12 -prec_ppm "${precursor_ion_tol_units}" 14 -prec_ppm "${precursor_ion_tol_units}"
15 ### -digestion
16 ### multiple enzymes?
13 -enzyme "${enzyme}" 17 -enzyme "${enzyme}"
18 ### -specificity
14 #set $fixed_mods_str = $fixed_modifications or '' 19 #set $fixed_mods_str = $fixed_modifications or ''
15 #set $variable_mods_str = $variable_modifications or '' 20 #set $variable_mods_str = $variable_modifications or ''
16 #if $fixed_mods_str 21 #if $fixed_mods_str
17 -fixed_mods "$fixed_mods_str" 22 -fixed_mods "$fixed_mods_str"
18 #end if 23 #end if
19 #if $variable_mods_str 24 #if $variable_mods_str
20 -variable_mods "$variable_mods_str" 25 -variable_mods "$variable_mods_str"
21 #end if 26 #end if
22 -min_charge $min_charge 27 -min_charge $min_charge
23 -max_charge $max_charge 28 -max_charge $max_charge
29 ### value per enzyme
24 -mc $missed_cleavages 30 -mc $missed_cleavages
25 -fi $forward_ion 31 -fi $forward_ion
26 -ri $reverse_ion 32 -ri $reverse_ion
27 </token> 33 </token>
28 <token name="@SEARCHGUI_MAJOR_VERSION@">2</token> 34 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
29 <token name="@SEARCHGUI_VERSION@">2.9</token> 35 <token name="@SEARCHGUI_VERSION@">3.1.4</token>
30 <xml name="general_options"> 36 <xml name="general_options">
31 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" 37 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
32 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> 38 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
33 <option value="1">Parts per million (ppm)</option> 39 <option value="1">Parts per million (ppm)</option>
34 <option value="2">Daltons</option> 40 <option value="2">Daltons</option>