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comparison maxquant.xml @ 0:d4b6c9eae635 draft

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Initial commit.
author galaxyp
date Fri, 10 May 2013 17:22:51 -0400
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-1:000000000000 0:d4b6c9eae635
1 <tool id="maxquant" version="0.1.0" name="MaxQuant">
2 <description>
3 </description>
4 <requirements>
5 <requirement>maxquant</requirement>
6 <requirement type="platform">windows</requirement>
7 </requirements>
8 <configfiles>
9 <configfile name="inputs_config">##Describe inputs
10 #set $type = str($analysis_type.type)
11 #if $type == "single"
12 #set $groups = [$analysis_type]
13 #elif $type == "multi_same"
14 #set $groups = $analysis_type.groups
15 #end if
16 #for $i, $group in enumerate($groups)
17 num:${str(i + 1)}
18 #for $input in $group.inputs
19 name:${input.display_name}
20 path:${input}
21 #end for
22 #end for
23 </configfile>
24 </configfiles>
25 <command interpreter="python">maxquant_wrapper.py
26 --input_groups=$inputs_config
27 --database="${database}"
28 --database_name="${database.name}"
29 --protease=$analysis_type.protease
30 --first_search_tol=$analysis_type.first_search_tol
31 --main_search_tol=$analysis_type.main_search_tol
32 --max_missed_cleavages=$analysis_type.max_missed_cleavages
33 --max_n_mods=$analysis_type.max_n_mods
34 --variable_mods="${analysis_type.variable_modifications or ''}"
35 #if $analysis_type.advanced_group_parameters.specify
36 --do_mass_filtering=$analysis_type.advanced_group_parameters.do_mass_filtering
37 --max_charge=$analysis_type.advanced_group_parameters.max_charge
38 #end if
39 #set $run = $analysis_type.run
40 #set $lcms_run_type = $run.lcms_run_type
41 --lcms_run_type=$lcms_run_type
42 #if str($lcms_run_type) != "3"
43 ## i.e. is not reporter ion type
44 #if $run.labels_conditional.labeled
45 #for $label_group in $run.labels_conditional.label_groups
46 --labels="${label_group.labels or ''}"
47 #end for
48 --max_labeled_aa=$run.labels_conditional.max_labeled_aa
49 #end if
50 #else
51 --reporter_type=$run.reporter_type
52 #end if
53 #set $sp = $advanced_sequence_parameters
54 #if $sp.specify
55 --include_contamiants=${str(sp['include_contamiants']).lower()}
56 --equal_il=${str(sp['equal_il']).lower()}
57 --randomize=${str(sp['randomize'])}
58 #end if
59 #if $quantification.specify
60 #set $restrict = $quantification.restrict.restrict_protein_quantification
61 --restrict_protein_quantification=${str(restrict).lower()}
62 #if $quantification.restrict.restrict_protein_quantification
63 --restrict_mods="${quantification.restrict.restrict_modifications or ''}"
64 #end if
65 --quant_mode=$quantification.quant_mode
66 --use_counterparts=$quantification.use_counterparts
67 --min_ratio_count=$quantification.min_ratio_count
68 #end if
69 #if $site_quantification.specify
70 --site_quant_mode=$site_quantification.site_quant_mode
71 --use_norm_ratios_for_occupancy=$site_quantification.use_norm_ratios_for_occupancy
72 #end if
73 #set $identification_type = str($identification.options_type)
74 #if $identification_type != "none"
75 --protein_fdr=$identification.protein_fdr
76 --peptide_fdr=$identification.peptide_fdr
77 --site_fdr=$identification.site_fdr
78 #if $identification_type != "simple"
79 --peptide_pep=$identification.peptide_pep
80 #end if
81 #end if
82 #if $misc.specify
83 --re_quantify="$misc.re_quantify"
84 #end if
85 --fixed_mods="${fixed_modifications or ''}"
86 --output_protein_groups=$output_protein_groups
87 --output_peptides=$output_peptides
88 --output_evidence=$output_evidence
89 --output_parameters=$output_parameters
90 --output_msms=$output_msms
91 --output_mqpar=$output_mqpar
92 </command>
93 <macros>
94 <macro name="input_param">
95 <param format="raw" multiple="true" name="inputs" type="data" label="RAW Inputs" help="" />
96 </macro>
97 <macro name="mod_opts">
98 <options from_file="maxquant_mods.loc">
99 <column name="name" index="0"/>
100 <column name="value" index="0" />
101 </options>
102 <sanitizer>
103 <valid>
104 <add value="&lt;"/>
105 <add value="&gt;"/>
106 <add value="["/>
107 <add value="]"/>
108 </valid>
109 </sanitizer>
110 </macro>
111 <macro name="protease_opts">
112 <options from_file="maxquant_proteases.loc">
113 <column name="name" index="0"/>
114 <column name="value" index="0" />
115 </options>
116 </macro>
117 <macro name="group_params">
118 <param name="protease" label="Enzyme" type="select">
119 <expand macro="protease_opts" />
120 </param>
121 <param name="first_search_tol" label="First Search Tolerance (ppm)" type="float" value="20" />
122 <param name="main_search_tol" label="Main Search Tolerance (ppm)" type="float" value="6" />
123 <param name="max_n_mods" type="integer" label="Maximum Number of Modifications per Peptide" value="5" />
124 <param name="max_missed_cleavages" type="integer" label="Maximum Number of Missed Cleavages" value="2" />
125 <param name="variable_modifications" label="Variable Modifications" type="select" multiple="true">
126 <expand macro="mod_opts" />
127 </param>
128 <conditional name="run">
129 <param name="lcms_run_type" type="select" label="Run Type">
130 <option value="0">Standard</option>
131 <option value="2">All ion fragmentation</option>
132 <option value="3">Reporter ion</option>
133 </param>
134 <when value="0">
135 <expand macro="labels" />
136 </when>
137 <when value="2">
138 <expand macro="labels" />
139 </when>
140 <when value="3">
141 <expand macro="reporter" />
142 </when>
143 </conditional>
144 <conditional name="advanced_group_parameters">
145 <param name="specify" type="boolean" label="Specify Advanced Group Parameters" checked="false" />
146 <when value="false">
147 </when>
148 <when value="true">
149 <param name="do_mass_filtering" type="boolean" label="Individual Peptide Mass Tolerances" checked="true" truevalue="true" falsevalue="false" />
150 <param name="max_charge" type="integer" label="Maximum Charge" value="7" />
151 <!--
152 TODO: First charge protease, first charge mods.
153 -->
154 </when>
155 </conditional>
156 </macro>
157 <macro name="labels">
158 <conditional name="labels_conditional">
159 <param name="labeled" type="boolean" label="Specify Labels" checked="false" />
160 <when value="false">
161 </when>
162 <when value="true">
163 <repeat name="label_groups" title="Label Groups">
164 <param name="labels" type="select" title="Labels" multiple="true" help="Select none to describe unlabelled 'light labels'.">
165 <option value="Arg6">Arg6</option>
166 <option value="Arg10">Arg10</option>
167 <option value="Lys4">Lys4</option>
168 <option value="Lys6">Lys6</option>
169 <option value="Lys8">Lys8</option>
170 </param>
171 </repeat>
172 <param name="max_labeled_aa" type="integer" title="Max Labeled Amino Acids" value="3" />
173 </when>
174 </conditional>
175 </macro>
176 <macro name="reporter">
177 <param name="reporter_type" type="select" label="Reporter Ions Type">
178 <option value="itraq_4plex">4-plex iTRAQ</option>
179 <option value="itraq_8plex">8-plex iTRAQ</option>
180 <option value="tmt_2plex">2-plex TMT</option>
181 <option value="tmt_6plex">6-plex TMT</option>
182 </param>
183 </macro>
184 <macro name="advanced_group_conditional">
185
186 </macro>
187 <macro name="advanced_sequences_conditional">
188 <conditional name="advanced_sequence_parameters">
189 <param name="specify" type="boolean" label="Specify Advanced Sequence Parameters" checked="false" />
190 <when value="false">
191 </when>
192 <when value="true">
193 <param name="include_contamiants" type="boolean" label="Include Contamiant Sequences" checked="true" />
194 <param name="equal_il" type="boolean" label="I = L" checked="false" />
195 <param name="randomize" type="select" label="Decoy Type">
196 <option value="false" selected="true">Reverse</option>
197 <option value="true">Randomize</option>
198 </param>
199 <!-- TODO: special_aas, KR -->
200 </when>
201 </conditional>
202 </macro>
203 <macro name="identification_conditional">
204 <conditional name="identification">
205 <param name="options_type" type="select" label="Specify Identification Parameters">
206 <option value="none">None, use all defaults.</option>
207 <option value="simple">Simple, specify a few high level parameters.</option>
208 <option value="advanced">Advanced, specify many identification parameters.</option>
209 </param>
210 <when value="none">
211 </when>
212 <when value="simple">
213 <expand macro="simple_identification_params" />
214 </when>
215 <when value="advanced">
216 <expand macro="simple_identification_params" />
217 <expand macro="advanced_identification_params" />
218 </when>
219 </conditional>
220 </macro>
221 <macro name="site_quantification_conditional">
222 <conditional name="site_quantification">
223 <param name="specify" type="boolean" label="Specify Advanced Site Quantification Parameters" checked="false" />
224 <when value="false">
225 </when>
226 <when value="true">
227 <param name="site_quant_mode" type="select" label="Site Quantification Mode">
228 <!-- TODO verify values -->
229 <option value="0" selected="true">Use least modified peptides</option>
230 <option value="1">Use largest change</option>
231 </param>
232 <param name="use_norm_ratios_for_occupancy" type="boolean" label="Use normalized Ratios for Occupancy" truevalue="true" falsevalue="false" checked="true"/>
233 </when>
234 </conditional>
235 </macro>
236 <macro name="protein_quantification_conditional">
237 <conditional name="quantification">
238 <param name="specify" type="boolean" label="Specify Advanced Protein Quantification Parameters" checked="false" />
239 <when value="false">
240 </when>
241 <when value="true">
242 <conditional name="restrict">
243 <param name="restrict_protein_quantification" type="boolean" label="Restrict Protein Quantification" checked="true" help="to unmodified peptides and those with certain modifications."/>
244 <when value="false">
245 </when>
246 <when value="true">
247 <param name="restrict_modifications" label="Modifications for Quantification" type="select" help="If advanced protein quantification parameters is not selected these default to Oxidation (M) and Actetyl (Protein N-term), but they must be selected (if desired) in this mode." multiple="true">
248 <expand macro="mod_opts" />
249 </param>
250 </when>
251 </conditional>
252 <param name="quant_mode" type="select" label="Protein Quantification Mode">
253 <option value="0">Use all peptides</option>
254 <option value="1" selected="true">Use razor and unique peptides</option>
255 <option value="2">Use unique peptides</option>
256 </param>
257 <param name="use_counterparts" type="boolean" label="Discard Unmodified Counterpart Peptides." checked="true" truevalue="false" falsevalue="true" />
258 <param name="min_ratio_count" label="Minimum Ratio Count" value="2" type="integer" />
259 </when>
260 </conditional>
261 </macro>
262 <macro name="simple_identification_params">
263 <param name="protein_fdr" label="Protein FDR" value="0.01" type="float" />
264 <param name="peptide_fdr" label="Peptide FDR" value="0.01" type="float" />
265 <param name="site_fdr" label="Protein FDR" value="0.01" type="float" />
266 </macro>
267 <macro name="advanced_identification_params">
268 <param name="peptide_pep" label="Max Peptide PEP" value="1" type="float" />
269 <!-- TODO: Apply site FDR seperately (boolean), Min peptides, Min Score,
270 min peptide length, min razor + unique peptides, filter labeled aa,
271 min unique peptides, second peptides (boolean true) -->
272 </macro>
273 <macro name="misc_conditional">
274 <conditional name="misc">
275 <param name="specify" type="boolean" label="Specify Misc Parameters" checked="false" />
276 <when value="false">
277 </when>
278 <when value="true">
279 <param name="re_quantify" type="boolean" label="Re-quantify" checked="true" truevalue="true" falsevalue="false" />
280 <!--
281 "Keep low-scoring versions of identified peptides" 0 = No, 1 only within parameters groups, 2 = Also between parameter groups.
282 Match Between Runs: bool
283 Time window (minutes): 2
284 Label-free quantification:
285 LFO min ratio count 2
286 Fast LFQ
287 iBAQ
288 Log fit
289 -->
290 </when>
291 </conditional>
292 </macro>
293 </macros>
294 <inputs>
295 <conditional name="analysis_type">
296 <param name="type" type="select" value="single" help="The wrapper has not yet implemented multiple groups with different parameters">
297 <option value="single">Single Group</option>
298 <option value="multi_same">Multi-Group Identical Parameters</option>
299 </param>
300 <when value="multi_same">
301 <repeat name="groups">
302 <expand macro="input_param" />
303 </repeat>
304 <expand macro="group_params" />
305 </when>
306 <when value="single">
307 <expand macro="input_param" />
308 <expand macro="group_params" />
309 </when>
310 </conditional>
311 <param format="fasta" name="database" type="data" label="FASTA Database" help="" />
312 <expand macro="advanced_sequences_conditional" />
313 <param name="fixed_modifications" label="Fixed Modifications" type="select" multiple="true">
314 <expand macro="mod_opts" />
315 </param>
316 <expand macro="identification_conditional" />
317 <expand macro="protein_quantification_conditional" />
318 <expand macro="site_quantification_conditional" />
319 <expand macro="misc_conditional" />
320 </inputs>
321 <outputs>
322 <data format="tabular" name="output_protein_groups" label="MaxQuant Protein Groups for ${on_string}"/>
323 <data format="tabular" name="output_peptides" label="MaxQuant Peptides for ${on_string}"/>
324 <data format="tabular" name="output_evidence" label="MaxQuant Evidence for ${on_string}"/>
325 <data format="tabular" name="output_parameters" label="MaxQuant Tabular Parameters for ${on_string}"/>
326 <data format="tabular" name="output_msms" label="MaxQuant MSMS for ${on_string}"/>
327 <data format="tabular" name="output_mqpar" label="MaxQuant Parameters XML for ${on_string}"/>
328 </outputs>
329 <help>
330 </help>
331 </tool>