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comparison macros.xml @ 43:7963340ab569 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
author galaxyp
date Mon, 05 Mar 2018 10:09:34 -0500
parents 9e20c34298e3
children 5fa8b409599e
comparison
equal deleted inserted replaced
42:9e20c34298e3 43:7963340ab569
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.*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 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
8 </stdio> 8 </stdio>
9 </xml> 9 </xml>
10 <token name="@GENERAL_PARAMETERS@"> 10 <token name="@GENERAL_PARAMETERS@">
15 15
16 -min_charge $precursor_options.min_charge 16 -min_charge $precursor_options.min_charge
17 -max_charge $precursor_options.max_charge 17 -max_charge $precursor_options.max_charge
18 -fi $precursor_options.forward_ion 18 -fi $precursor_options.forward_ion
19 -ri $precursor_options.reverse_ion 19 -ri $precursor_options.reverse_ion
20 -min_isotope ${precursor_options.min_isotope} 20 -min_isotope ${precursor_options.min_isotope}
21 -max_isotope ${precursor_options.max_isotope} 21 -max_isotope ${precursor_options.max_isotope}
22 #if $protein_digest_options.digestion.cleavage == 'default': 22 #if $protein_digest_options.digestion.cleavage == 'default':
23 ## -enzyme "Trysin" 23 ## -enzyme "Trysin"
24 -mc $protein_digest_options.digestion.missed_cleavages 24 -mc $protein_digest_options.digestion.missed_cleavages
25 #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0: 25 #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
26 #set $enzymes = [] 26 #set $enzymes = []
28 ## #set $specificities = [] 28 ## #set $specificities = []
29 #for $i, $digest in enumerate($protein_digest_options.digestion.digests): 29 #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
30 #silent $enzymes.append(str($digest.enzyme)) 30 #silent $enzymes.append(str($digest.enzyme))
31 #silent $missed_cleavages.append(str($digest.missed_cleavages)) 31 #silent $missed_cleavages.append(str($digest.missed_cleavages))
32 ## #silent $specificities.append(str($digest.specificity)) 32 ## #silent $specificities.append(str($digest.specificity))
33 #end for 33 #end for
34 -enzyme "#echo ','.join($enzymes)#" 34 -enzyme "#echo ','.join($enzymes)#"
35 -mc "#echo ','.join($missed_cleavages)#" 35 -mc "#echo ','.join($missed_cleavages)#"
36 ## -specificity "#echo ','.join($specificities)#" 36 ## -specificity "#echo ','.join($specificities)#"
37 #else: 37 #else:
38 -digestion $protein_digest_options.digestion.cleavage 38 -digestion $protein_digest_options.digestion.cleavage
39 #end if 39 #end if
40 40
41 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or '' 41 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
42 #set $variable_mods_str = $protein_modification_options.variable_modifications or '' 42 #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
43 #if $fixed_mods_str 43 #if $fixed_mods_str
44 -fixed_mods "$fixed_mods_str" 44 -fixed_mods "$fixed_mods_str"
45 #end if 45 #end if
46 #if $variable_mods_str 46 #if $variable_mods_str
47 -variable_mods "$variable_mods_str" 47 -variable_mods "$variable_mods_str"
48 #end if 48 #end if
49 49
77 <option value="Lys-C, no P rule">Lys-C, no P rule</option> 77 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
78 <option value="Pepsin A">Pepsin A</option> 78 <option value="Pepsin A">Pepsin A</option>
79 <option value="Trypsin + CNBr">Trypsin + CNBr</option> 79 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
80 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> 80 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
81 <option value="Trypsin, no P rule">Trypsin, no P rule</option> 81 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
82 <option value="Whole Protein">Whole Protein</option> 82 <option value="Whole Protein">Whole Protein</option>
83 <option value="Asp-N">Asp-N</option> 83 <option value="Asp-N">Asp-N</option>
84 <option value="Glu-C">Glu-C</option> 84 <option value="Glu-C">Glu-C</option>
85 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> 85 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
86 <option value="Top-Down">Top-Down</option> 86 <option value="Top-Down">Top-Down</option>
87 <option value="Semi-Tryptic">Semi-Tryptic</option> 87 <option value="Semi-Tryptic">Semi-Tryptic</option>
127 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance" 127 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
128 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> 128 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
129 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units" 129 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
130 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> 130 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
131 <option value="1">Parts per million (ppm)</option> 131 <option value="1">Parts per million (ppm)</option>
132 <option value="0">Daltons</option> 132 <option value="0" selected="true">Daltons</option>
133 </param> 133 </param>
134 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance" 134 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
135 help="Provide error value for fragment ions, based on instrument used"/> 135 help="Provide error value for fragment ions, based on instrument used"/>
136 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> 136 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
137 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> 137 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
155 <options from_file="searchgui_mods.loc"> 155 <options from_file="searchgui_mods.loc">
156 <column name="name" index="0" /> 156 <column name="name" index="0" />
157 <column name="value" index="0" /> 157 <column name="value" index="0" />
158 </options> 158 </options>
159 </param> 159 </param>
160 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 160 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
161 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> 161 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
162 <options from_file="searchgui_mods.loc"> 162 <options from_file="searchgui_mods.loc">
163 <column name="name" index="0" /> 163 <column name="name" index="0" />
164 <column name="value" index="0" /> 164 <column name="value" index="0" />
165 </options> 165 </options>