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comparison macros.xml @ 2:eea7e945f479 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
author jjohnson
date Thu, 12 Jul 2018 08:42:58 -0400
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children 8cf04d7a6683
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1:fa76abf69433 2:eea7e945f479
1 <macros>
2 <xml name="stdio">
3 <stdio>
4 <exit_code range="1:" level="fatal" description="Job Failed" />
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"/>
7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
8 </stdio>
9 </xml>
10 <token name="@ENZYMESCLI@"><![CDATA[
11 #if len($protein_digest_options.digestion.user_enzymes) > 0:
12 #for $i, $user_enzyme in enumerate($protein_digest_options.digestion.user_enzymes):
13 (searchgui com.compomics.cli.enzymes.EnzymesCLI -out enzymes.json -in enzymes.json
14 -name $user_enzyme.enzyme_name
15 #if $user_enzyme.cleave_before:
16 -cleave_before $user_enzyme.cleave_before
17 #end if
18 #if $user_enzyme.cleave_after:
19 -cleave_after $user_enzyme.cleave_after
20 #end if
21 #if $user_enzyme.restriction_before:
22 -restriction_before $user_enzyme.restriction_before
23 #end if
24 #if $user_enzyme.restriction_after:
25 -restriction_after $user_enzyme.restriction_after
26 #end if
27 ) &&
28 #end for
29 #end if
30 ]]></token>
31 <token name="@ENZYME_CONFIGUTRATION@">
32 #if len($protein_digest_options.digestion.user_enzymes) > 0:
33 -enzyme_configuration enzymes.json
34 #end if
35 </token>
36 <token name="@GENERAL_PARAMETERS@">
37 -frag_tol '${precursor_options.fragment_tol}'
38 -frag_ppm '${precursor_options.fragment_tol_units}'
39 -prec_tol '${precursor_options.precursor_ion_tol}'
40 -prec_ppm '${precursor_options.precursor_ion_tol_units}'
41
42 -min_charge $precursor_options.min_charge
43 -max_charge $precursor_options.max_charge
44 -fi $precursor_options.forward_ion
45 -ri $precursor_options.reverse_ion
46 -min_isotope ${precursor_options.min_isotope}
47 -max_isotope ${precursor_options.max_isotope}
48 #if $protein_digest_options.digestion.cleavage == 'default':
49 ## -enzyme "Trysin"
50 -mc $protein_digest_options.digestion.missed_cleavages
51 #elif $protein_digest_options.digestion.cleavage == '0':
52 #set $enzymes = []
53 #set $missed_cleavages = []
54 ## #set $specificities = []
55 #if len($protein_digest_options.digestion.digests) > 0:
56 #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
57 #silent $enzymes.append(str($digest.enzyme))
58 #silent $missed_cleavages.append(str($digest.missed_cleavages))
59 ## #silent $specificities.append(str($digest.specificity))
60 #end for
61 #end if
62 #if len($protein_digest_options.digestion.user_enzymes) > 0:
63 #for $i, $user_enzyme in enumerate($protein_digest_options.digestion.user_enzymes):
64 #silent $enzymes.append(str($user_enzyme.enzyme_name))
65 #silent $missed_cleavages.append(str($user_enzyme.missed_cleavages))
66 #end for
67 #end if
68 #if len($enzymes) > 0:
69 -enzyme "#echo ','.join($enzymes)#"
70 -mc "#echo ','.join($missed_cleavages)#"
71 ## -specificity "#echo ','.join($specificities)#"
72 #end if
73 #else:
74 -digestion $protein_digest_options.digestion.cleavage
75 #end if
76
77 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
78 #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
79 #if $fixed_mods_str
80 -fixed_mods "$fixed_mods_str"
81 #end if
82 #if $variable_mods_str
83 -variable_mods "$variable_mods_str"
84 #end if
85
86 </token>
87 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
88 <token name="@SEARCHGUI_VERSION@">3.3.3</token>
89 <xml name="general_options">
90
91 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
92 <conditional name="digestion">
93 <param name="cleavage" type="select" label="Digestion">
94 <option value="default" selected="true">Trypsin</option>
95 <option value="0">Select Enzymes</option>
96 <option value="1">Unspecific Cleavage</option>
97 <option value="2">Whole Protein</option>
98 </param>
99 <when value="default">
100 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
101 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
102 </when>
103 <when value="0">
104 <repeat name="digests" min="1" title="Enzymes">
105 <param name="enzyme" type="select" label="Enzyme"
106 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
107 <option value="Trypsin">Trypsin</option>
108 <option value="Arg-C">Arg-C</option>
109 <option value="CNBr">CNBr</option>
110 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
111 <option value="Formic Acid">Formic Acid</option>
112 <option value="Lys-C">Lys-C</option>
113 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
114 <option value="Pepsin A">Pepsin A</option>
115 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
116 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
117 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
118 <option value="Whole Protein">Whole Protein</option>
119 <option value="Asp-N">Asp-N</option>
120 <option value="Glu-C">Glu-C</option>
121 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
122 <option value="Top-Down">Top-Down</option>
123 <option value="Semi-Tryptic">Semi-Tryptic</option>
124 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
125 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
126 <option value="Asp-N (DE)">Asp-N (DE)</option>
127 <option value="Glu-C (DE)">Glu-C (DE)</option>
128 <option value="Lys-N (K)">Lys-N (K)</option>
129 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
130 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
131 <option value="Semi-Glu-C">Semi-Glu-C</option>
132 <option value="LysargiNase">LysargiNase</option>
133 <option value="Semi-LysargiNase">Semi-LysargiNase</option>
134 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
135 <option value="Semi-Arg-C">Semi-Arg-C</option>
136 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
137 <option value="Arg-N">Arg-N</option>
138 <option value="Semi-Arg-N">Semi-Arg-N</option>
139 </param>
140 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
141 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
142 <!--
143 <param name="specificity" type="select" label="Specificity">
144 <option value="0" selected="true">Specific at both termini</option>
145 <option value="1">Semi-Specific - one terminus</option>
146 <option value="2">Specific at the N-terminus only</option>
147 <option value="3">Specific at the C-terminus only</option>
148 </param>
149 -->
150 </repeat>
151 </when>
152 <when value="1"/>
153 <when value="2"/>
154 </conditional>
155 </section>
156
157 <section name="precursor_options" expanded="false" title="Precursor Options">
158 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
159 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
160 <option value="1">Parts per million (ppm)</option>
161 <option value="0">Daltons</option>
162 </param>
163 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
164 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
165 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
166 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
167 <option value="1">Parts per million (ppm)</option>
168 <option value="0" selected="true">Daltons</option>
169 </param>
170 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
171 help="Provide error value for fragment ions, based on instrument used"/>
172 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
173 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
174 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
175 <option value="a">a</option>
176 <option value="b" selected="true">b</option>
177 <option value="c">c</option>
178 </param>
179 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
180 <option value="x">x</option>
181 <option value="y" selected="true">y</option>
182 <option value="z">z</option>
183 </param>
184 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
185 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
186 </section>
187
188 <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
189 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
190 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
191 <options from_file="searchgui_mods.loc">
192 <column name="name" index="0" />
193 <column name="value" index="0" />
194 </options>
195 </param>
196 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
197 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
198 <options from_file="searchgui_mods.loc">
199 <column name="name" index="0" />
200 <column name="value" index="0" />
201 </options>
202 </param>
203 </section>
204
205 </xml>
206
207 <xml name="citations">
208 <citations>
209 <citation type="doi">10.1186/1471-2105-12-70</citation>
210 <citation type="doi">10.1002/pmic.201000595</citation>
211 <citation type="doi">doi:10.1038/nbt.3109</citation>
212 </citations>
213 </xml>
214
215 </macros>