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comparison maxquant.xml @ 1:8bac3cc5c5de draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 05:01:05 -0400
parents d4b6c9eae635
children 175e062b6a17
comparison
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0:d4b6c9eae635 1:8bac3cc5c5de
1 <tool id="maxquant" version="0.1.0" name="MaxQuant"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@">
2 <description> 2 <macros>
3 </description> 3 <import>macros.xml</import>
4 <requirements> 4 </macros>
5 <requirement>maxquant</requirement> 5 <requirements>
6 <requirement type="platform">windows</requirement> 6 <requirement type="package" version="@VERSION@">maxquant</requirement>
7 </requirements> 7 <requirement type="package" version="3.7">python</requirement>
8 <configfiles> 8 </requirements>
9 <configfile name="inputs_config">##Describe inputs 9 <command detect_errors="exit_code"><![CDATA[
10 #set $type = str($analysis_type.type) 10 #import re
11 #if $type == "single" 11
12 #set $groups = [$analysis_type] 12 python3 '$__tool_directory__/mqwrapper.py'
13 #elif $type == "multi_same" 13 --num_threads=\${GALAXY_SLOTS:-1}
14 #set $groups = $analysis_type.groups 14 --substitution_rx='@SUBSTITUTION_RX@'
15 #end if 15 #if $input_opts.infile.select == "mzxml_files"
16 #for $i, $group in enumerate($groups) 16 --mzxml_files='$input_opts.infile.mzxml_files'
17 num:${str(i + 1)} 17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.mzxml_files])
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=$run.labels_conditional.max_labeled_aa
49 #end if
50 #else 18 #else
51 --reporter_type=$run.reporter_type 19 --raw_files='$input_opts.infile.raw_files'
52 #end if 20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.raw_files])
53 #set $sp = $advanced_sequence_parameters 21 #end if
54 #if $sp.specify 22 --infile_names='$names'
55 --include_contamiants=${str(sp['include_contamiants']).lower()} 23 --version='@VERSION@'
56 --equal_il=${str(sp['equal_il']).lower()} 24 --fasta_files='$input_opts.fasta_files'
57 --randomize=${str(sp['randomize'])} 25 --identifier_parse_rule='$input_opts.identifier_parse_rule'
58 #end if 26 --description_parse_rule='$input_opts.description_parse_rule'
59 #if $quantification.specify 27
60 #set $restrict = $quantification.restrict.restrict_protein_quantification 28 --exp_design='$search_opts.template'
61 --restrict_protein_quantification=${str(restrict).lower()} 29 --missed_cleavages=$search_opts.missed_cleavages
62 #if $quantification.restrict.restrict_protein_quantification 30 --min_peptide_len=$search_opts.min_peptide_len
63 --restrict_mods="${quantification.restrict.restrict_modifications or ''}" 31 --max_peptide_mass=$search_opts.max_peptide_mass
64 #end if 32 --min_unique_pep=$search_opts.min_unique_pep
65 --quant_mode=$quantification.quant_mode 33 $search_opts.calc_peak_properties
66 --use_counterparts=$quantification.use_counterparts 34 $search_opts.match_between_runs
67 --min_ratio_count=$quantification.min_ratio_count 35 #if $search_opts.fixed_mods
68 #end if 36 --fixed_mods='$search_opts.fixed_mods'
69 #if $site_quantification.specify 37 #end if
70 --site_quant_mode=$site_quantification.site_quant_mode 38 #if $search_opts.var_mods
71 --use_norm_ratios_for_occupancy=$site_quantification.use_norm_ratios_for_occupancy 39 --var_mods='$search_opts.var_mods'
72 #end if 40 #end if
73 #set $identification_type = str($identification.options_type) 41 #if $search_opts.proteases
74 #if $identification_type != "none" 42 --proteases='$search_opts.proteases'
75 --protein_fdr=$identification.protein_fdr 43 #end if
76 --peptide_fdr=$identification.peptide_fdr 44 #if $search_opts.silac.light_mods
77 --site_fdr=$identification.site_fdr 45 --light_mods='$search_opts.silac.light_mods'
78 #if $identification_type != "simple" 46 #end if
79 --peptide_pep=$identification.peptide_pep 47 #if $search_opts.silac.medium_mods
80 #end if 48 --medium_mods='$search_opts.silac.medium_mods'
81 #end if 49 #end if
82 #if $misc.specify 50 #if $search_opts.silac.heavy_mods
83 --re_quantify="$misc.re_quantify" 51 --heavy_mods='$search_opts.silac.heavy_mods'
84 #end if 52 #end if
85 --fixed_mods="${fixed_modifications or ''}" 53 #if $search_opts.lfq.do_lfq == "--lfq_mode=1"
86 --output_protein_groups=$output_protein_groups 54 $search_opts.lfq.do_lfq.lfq_mode
87 --output_peptides=$output_peptides 55 --lfq_min_ratio_count=$search_opts.lfq.do_lfq.lfq_min_ratio_count
88 --output_evidence=$output_evidence 56 --lfq_min_edges_per_node=$search_opts.lfq.do_lfq.lfq_min_edges_per_node
89 --output_parameters=$output_parameters 57 --lfq_avg_edges_per_node=$search_opts.lfq.do_lfq.lfq_avg_edges_per_node
90 --output_msms=$output_msms 58 $search_opts.lfq.do_lfq.lfq_skip_norm
91 --output_mqpar=$output_mqpar 59 $search_opts.lfq.do_lfq.separate_lfq
92 </command> 60 $search_opts.lfq.do_lfq.lfq_stabilize_large_ratios
93 <macros> 61 $search_opts.lfq.do_lfq.lfq_require_msms
94 <macro name="input_param"> 62 #if $search_opts.lfq.do_lfq.do_ibaq == "--ibaq"
95 <param format="raw" multiple="true" name="inputs" type="data" label="RAW Inputs" help="" /> 63 $search_opts.lfq.do_lfq.do_ibaq.ibaq
96 </macro> 64 $search_opts.lfq.do_lfq.do_ibaq.ibaq_log_fit
97 <macro name="mod_opts"> 65 #end if
98 <options from_file="maxquant_mods.loc"> 66 $search_opts.lfq.do_lfq.advanced_site_intensities
99 <column name="name" index="0"/> 67 #end if
100 <column name="value" index="0" /> 68
101 </options> 69 $output_opts.write_mztab
102 <sanitizer> 70 --evidence='$evidence'
103 <valid> 71 --msms='$msms'
104 <add value="&lt;"/> 72 --parameters='$parameters'
105 <add value="&gt;"/> 73 --peptides='$peptides'
106 <add value="["/> 74 --proteinGroups='$proteinGroups'
107 <add value="]"/> 75 --allPeptides='$allPeptides'
108 </valid> 76 --libraryMatch='$libraryMatch'
109 </sanitizer> 77 --matchedFeatures='$matchedFeatures'
110 </macro> 78 --modificationSpecificPeptides='$modificationSpecificPeptides'
111 <macro name="protease_opts"> 79 --ms3Scans='$ms3Scans'
112 <options from_file="maxquant_proteases.loc"> 80 --msmsScans='$msmsScans'
113 <column name="name" index="0"/> 81 --mzRange='$mzRange'
114 <column name="value" index="0" /> 82 --peptideSection='$peptideSection'
115 </options> 83 --summary='$summary'
116 </macro> 84 --mzTab='$mzTab'
117 <macro name="group_params"> 85 --mqpar_out='$mqpar_out'
118 <param name="protease" label="Enzyme" type="select"> 86
119 <expand macro="protease_opts" /> 87 #if 'log' in $output_opts.output
120 </param> 88 > '$log'
121 <param name="first_search_tol" label="First Search Tolerance (ppm)" type="float" value="20" /> 89 #end if
122 <param name="main_search_tol" label="Main Search Tolerance (ppm)" type="float" value="6" /> 90 #if 'output_all' in $output_opts.output
123 <param name="max_n_mods" type="integer" label="Maximum Number of Modifications per Peptide" value="5" /> 91 && tar -zcf '$output_all' ./combined/txt
124 <param name="max_missed_cleavages" type="integer" label="Maximum Number of Missed Cleavages" value="2" /> 92 #end if
125 <param name="variable_modifications" label="Variable Modifications" type="select" multiple="true"> 93 ]]></command>
126 <expand macro="mod_opts" /> 94 <inputs>
127 </param> 95 <section name="input_opts" title="Input Options" expanded="True">
128 <conditional name="run"> 96 <conditional name="infile">
129 <param name="lcms_run_type" type="select" label="Run Type"> 97 <param name="select" type="select" label="choose the type of your input files">
130 <option value="0">Standard</option> 98 <option value="raw_files">Thermo.raw</option>
131 <option value="2">All ion fragmentation</option> 99 <option value="mzxml_files">mzXML</option>
132 <option value="3">Reporter ion</option> 100 </param>
133 </param> 101 <when value="raw_files">
134 <when value="0"> 102 <param multiple="true" name="raw_files" type="data"
135 <expand macro="labels" /> 103 format="thermo.raw" label="RAW Files"
136 </when> 104 help="Specify one or more Thermo RAW files" />
137 <when value="2"> 105 </when>
138 <expand macro="labels" /> 106 <when value="mzxml_files">
139 </when> 107 <param multiple="true" name="mzxml_files" type="data"
140 <when value="3"> 108 format="mzxml" label="mzXML Files"
141 <expand macro="reporter" /> 109 help="Specify one or more mzXML files" />
142 </when> 110 </when>
143 </conditional> 111 </conditional>
144 <conditional name="advanced_group_parameters"> 112 <param format="fasta" multiple="true" name="fasta_files"
145 <param name="specify" type="boolean" label="Specify Advanced Group Parameters" checked="false" /> 113 type="data" label="FASTA files"
146 <when value="false"> 114 help="Specify one or more FASTA databases." />
147 </when> 115 <param name="identifier_parse_rule" type="text"
148 <when value="true"> 116 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
149 <param name="do_mass_filtering" type="boolean" label="Individual Peptide Mass Tolerances" checked="true" truevalue="true" falsevalue="false" /> 117 <sanitizer>
150 <param name="max_charge" type="integer" label="Maximum Charge" value="7" /> 118 <valid initial="string.printable">
151 <!-- 119 <remove value="&apos;"/>
152 TODO: First charge protease, first charge mods. 120 </valid>
153 --> 121 </sanitizer>
154 </when> 122 </param>
155 </conditional> 123 <param name="description_parse_rule" type="text"
156 </macro> 124 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
157 <macro name="labels"> 125 help="Modify parse rules if needed">
158 <conditional name="labels_conditional"> 126 <sanitizer>
159 <param name="labeled" type="boolean" label="Specify Labels" checked="false" /> 127 <valid initial="string.printable">
160 <when value="false"> 128 <remove value="&apos;"/>
161 </when> 129 </valid>
162 <when value="true"> 130 </sanitizer>
163 <repeat name="label_groups" title="Label Groups"> 131 </param>
164 <param name="labels" type="select" title="Labels" multiple="true" help="Select none to describe unlabelled 'light labels'."> 132 </section>
165 <option value="Arg6">Arg6</option> 133
166 <option value="Arg10">Arg10</option> 134 <section name="search_opts" title="Search Options" expanded="true">
167 <option value="Lys4">Lys4</option> 135 <param format="tabular" name="template" type="data" optional="true"
168 <option value="Lys6">Lys6</option> 136 label="Specify an experimental design template (if needed). For detailed
169 <option value="Lys8">Lys8</option> 137 instructions see the help text." />
170 </param> 138 <param type="integer" name="missed_cleavages"
171 </repeat> 139 label="missed cleavages" value="1"/>
172 <param name="max_labeled_aa" type="integer" title="Max Labeled Amino Acids" value="3" /> 140 <param type="integer" name="min_peptide_len"
173 </when> 141 label="minimum peptide length" value="7"/>
174 </conditional> 142 <param type="integer" name="max_peptide_mass"
175 </macro> 143 label="maximum peptide mass" value="4600"/>
176 <macro name="reporter"> 144 <param type="integer" name="min_unique_pep"
177 <param name="reporter_type" type="select" label="Reporter Ions Type"> 145 label="minimum unique peptides" value="1" />
178 <option value="itraq_4plex">4-plex iTRAQ</option> 146 <param name="calc_peak_properties" type="boolean" checked="false"
179 <option value="itraq_8plex">8-plex iTRAQ</option> 147 label="Calculate peak properties?"
180 <option value="tmt_2plex">2-plex TMT</option> 148 truevalue="--calc_peak_properties" falsevalue="" />
181 <option value="tmt_6plex">6-plex TMT</option> 149 <param name="match_between_runs" type="boolean" checked="false"
182 </param> 150 label="Match between runs?"
183 </macro> 151 truevalue="--match_between_runs" falsevalue="" />
184 <macro name="advanced_group_conditional"> 152 <param name="fixed_mods" type="select" label="fixed modifications"
185 153 multiple="true" help="select zero or more fixed modifications">
186 </macro> 154 <expand macro="modification"/>
187 <macro name="advanced_sequences_conditional"> 155 </param>
188 <conditional name="advanced_sequence_parameters"> 156 <param name="var_mods" type="select" label="variable modifications"
189 <param name="specify" type="boolean" label="Specify Advanced Sequence Parameters" checked="false" /> 157 multiple="true" help="select zero or more variable modifications">
190 <when value="false"> 158 <expand macro="modification"/>
191 </when> 159 </param>
192 <when value="true"> 160 <param name="proteases" type="select" label="proteases"
193 <param name="include_contamiants" type="boolean" label="Include Contamiant Sequences" checked="true" /> 161 multiple="true" help="select zero or more proteases">
194 <param name="equal_il" type="boolean" label="I = L" checked="false" /> 162 <expand macro="proteases"/>
195 <param name="randomize" type="select" label="Decoy Type"> 163 </param>
196 <option value="false" selected="true">Reverse</option> 164 <section title="label based quantitation" name="silac" expanded="false">
197 <option value="true">Randomize</option> 165 <param name="light_mods" type="select" label="light labels"
198 </param> 166 multiple="true" help="select zero or more light modifications">
199 <!-- TODO: special_aas, KR --> 167 <expand macro="label"/>
200 </when> 168 </param>
201 </conditional> 169 <param name="medium_mods" type="select" label="medium labels"
202 </macro> 170 multiple="true" help="select zero or more medium modifications">
203 <macro name="identification_conditional"> 171 <expand macro="label"/>
204 <conditional name="identification"> 172 </param>
205 <param name="options_type" type="select" label="Specify Identification Parameters"> 173 <param name="heavy_mods" type="select" label="heavy labels"
206 <option value="none">None, use all defaults.</option> 174 multiple="true" help="select zero or more heavy modifications">
207 <option value="simple">Simple, specify a few high level parameters.</option> 175 <expand macro="label"/>
208 <option value="advanced">Advanced, specify many identification parameters.</option> 176 </param>
209 </param> 177 </section>
210 <when value="none"> 178 <section title="label free quantification" name="lfq" expanded="false">
211 </when> 179 <conditional name="do_lfq">
212 <when value="simple"> 180 <param name="lfq_mode" type="select" label="Perform LFQ?">
213 <expand macro="simple_identification_params" /> 181 <option value="">No</option>
214 </when> 182 <option value="--lfq_mode=1">Yes</option>
215 <when value="advanced"> 183 </param>
216 <expand macro="simple_identification_params" /> 184 <when value="--lfq_mode=1">
217 <expand macro="advanced_identification_params" /> 185 <param type="integer" name="lfq_min_ratio_count"
218 </when> 186 label="LFQ minimum ratio count" value="2"/>
219 </conditional> 187 <param type="integer" name="lfq_min_edges_per_node"
220 </macro> 188 label="LFQ minimum number of neighbours" value="3"/>
221 <macro name="site_quantification_conditional"> 189 <param type="integer" name="lfq_avg_edges_per_node"
222 <conditional name="site_quantification"> 190 label="LFQ average number of neighbours" value="6"/>
223 <param name="specify" type="boolean" label="Specify Advanced Site Quantification Parameters" checked="false" /> 191 <param name="lfq_skip_norm" type="boolean" checked="false"
224 <when value="false"> 192 label="Skip normalization?"
225 </when> 193 truevalue="--lfq_skip_norm" falsevalue="" />
226 <when value="true"> 194 <param name="separate_lfq" type="boolean" checked="false"
227 <param name="site_quant_mode" type="select" label="Site Quantification Mode"> 195 label="Separate LFQ in parameter Groups?"
228 <!-- TODO verify values --> 196 truevalue="--separate_lfq" falsevalue="" />
229 <option value="0" selected="true">Use least modified peptides</option> 197 <param name="lfq_stabilize_large_ratios" type="boolean" checked="true"
230 <option value="1">Use largest change</option> 198 label="Stabilize large LFQ ratios?"
231 </param> 199 truevalue="--lfq_stabilize_large_ratios" falsevalue="" />
232 <param name="use_norm_ratios_for_occupancy" type="boolean" label="Use normalized Ratios for Occupancy" truevalue="true" falsevalue="false" checked="true"/> 200 <param name="lfq_require_msms" type="boolean" checked="true"
233 </when> 201 label="Require MS/MS for LFQ comparisons?"
234 </conditional> 202 truevalue="--lfq_require_msms" falsevalue="" />
235 </macro> 203 <conditional name="do_ibaq">
236 <macro name="protein_quantification_conditional"> 204 <param name="ibaq" type="select" label="iBAQ?">
237 <conditional name="quantification"> 205 <option value="">No</option>
238 <param name="specify" type="boolean" label="Specify Advanced Protein Quantification Parameters" checked="false" /> 206 <option value="--ibaq">Yes</option>
239 <when value="false"> 207 </param>
240 </when> 208 <when value="--ibaq">
241 <when value="true"> 209 <param name="ibaq_log_fit" type="boolean" checked="true"
242 <conditional name="restrict"> 210 label="Logarithmic fit?"
243 <param name="restrict_protein_quantification" type="boolean" label="Restrict Protein Quantification" checked="true" help="to unmodified peptides and those with certain modifications."/> 211 truevalue="--ibaq_log_fit" falsevalue="" />
244 <when value="false"> 212 </when>
245 </when> 213 <when value="">
246 <when value="true"> 214 </when>
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"> 215 </conditional>
248 <expand macro="mod_opts" /> 216 <param name="advanced_site_intensities" type="boolean" checked="true"
249 </param> 217 label="Advanced site intensities?"
250 </when> 218 truevalue="--advanced_site_intensities" falsevalue="" />
251 </conditional> 219 </when>
252 <param name="quant_mode" type="select" label="Protein Quantification Mode"> 220 <when value="">
253 <option value="0">Use all peptides</option> 221 </when>
254 <option value="1" selected="true">Use razor and unique peptides</option> 222 </conditional>
255 <option value="2">Use unique peptides</option> 223 </section>
256 </param> 224 </section>
257 <param name="use_counterparts" type="boolean" label="Discard Unmodified Counterpart Peptides." checked="true" truevalue="false" falsevalue="true" /> 225
258 <param name="min_ratio_count" label="Minimum Ratio Count" value="2" type="integer" /> 226 <section title="Output Options" name="output_opts" expanded="true">
259 </when> 227 <param name="write_mztab" type="boolean" checked="false"
260 </conditional> 228 label="Write mztab file?"
261 </macro> 229 truevalue="--write_mztab" falsevalue="" />
262 <macro name="simple_identification_params"> 230 <param type="select" name="output" label="Select the desired outputs."
263 <param name="protein_fdr" label="Protein FDR" value="0.01" type="float" /> 231 multiple="true" optional="false">
264 <param name="peptide_fdr" label="Peptide FDR" value="0.01" type="float" /> 232 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/>
265 <param name="site_fdr" label="Protein FDR" value="0.01" type="float" /> 233 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/>
266 </macro> 234 <expand macro="output_option" name="peptides" label="Peptides"/>
267 <macro name="advanced_identification_params"> 235 <expand macro="output_option" name="evidence" label="Evidence"/>
268 <param name="peptide_pep" label="Max Peptide PEP" value="1" type="float" /> 236 <expand macro="output_option" name="parameters" label="Tabular Paramters"/>
269 <!-- TODO: Apply site FDR seperately (boolean), Min peptides, Min Score, 237 <expand macro="output_option" name="msms" label="MSMS"/>
270 min peptide length, min razor + unique peptides, filter labeled aa, 238 <expand macro="output_option" name="mzTab" label="mzTab"/>
271 min unique peptides, second peptides (boolean true) --> 239 <expand macro="output_option" name="allPeptides" label="all peptides"/>
272 </macro> 240 <expand macro="output_option" name="libraryMatch" label="library match"/>
273 <macro name="misc_conditional"> 241 <expand macro="output_option" name="matchedFeatures" label="matched features"/>
274 <conditional name="misc"> 242 <expand macro="output_option" name="modificationSpecificPeptides" label="modification specific peptides"/>
275 <param name="specify" type="boolean" label="Specify Misc Parameters" checked="false" /> 243 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/>
276 <when value="false"> 244 <expand macro="output_option" name="msmsScans" label="msms scans"/>
277 </when> 245 <expand macro="output_option" name="mzRange" label="mz range"/>
278 <when value="true"> 246 <expand macro="output_option" name="peptideSection" label="peptide section"/>
279 <param name="re_quantify" type="boolean" label="Re-quantify" checked="true" truevalue="true" falsevalue="false" /> 247 <expand macro="output_option" name="summary" label="summary"/>
280 <!-- 248 <expand macro="output_option" name="output_all" label="complete 'combined/txt/' directory (compressed)"/>
281 "Keep low-scoring versions of identified peptides" 0 = No, 1 only within parameters groups, 2 = Also between parameter groups. 249 <expand macro="output_option" name="log" label="MaxQuant log"/>
282 Match Between Runs: bool 250 </param>
283 Time window (minutes): 2 251 </section>
284 Label-free quantification: 252 </inputs>
285 LFO min ratio count 2 253
286 Fast LFQ 254 <outputs>
287 iBAQ 255 <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/>
288 Log fit 256 <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/>
289 --> 257 <expand macro="output" name="peptides" label="MaxQuant Peptides"/>
290 </when> 258 <expand macro="output" name="evidence" label="MaxQuant Evidence"/>
291 </conditional> 259 <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/>
292 </macro> 260 <expand macro="output" name="msms" label="MaxQuant MSMS"/>
293 </macros> 261 <expand macro="output" name="mzTab" label="mzTab"/>
294 <inputs> 262 <expand macro="output" name="allPeptides" label="all peptides"/>
295 <conditional name="analysis_type"> 263 <expand macro="output" name="libraryMatch" label="library match"/>
296 <param name="type" type="select" value="single" help="The wrapper has not yet implemented multiple groups with different parameters"> 264 <expand macro="output" name="matchedFeatures" label="matched features"/>
297 <option value="single">Single Group</option> 265 <expand macro="output" name="modificationSpecificPeptides" label="modification specific peptides"/>
298 <option value="multi_same">Multi-Group Identical Parameters</option> 266 <expand macro="output" name="ms3Scans" label="ms3 scans"/>
299 </param> 267 <expand macro="output" name="msmsScans" label="msms Scans"/>
300 <when value="multi_same"> 268 <expand macro="output" name="mzRange" label="mz range"/>
301 <repeat name="groups"> 269 <expand macro="output" name="peptideSection" label="peptide section"/>
302 <expand macro="input_param" /> 270 <expand macro="output" name="summary" label="MaxQuant summary"/>
303 </repeat> 271 <expand macro="output" format="tar" name="output_all" label="'combined/txt/' directory"/>
304 <expand macro="group_params" /> 272 <expand macro="output" name="log" format="txt" label="log"/>
305 </when> 273 </outputs>
306 <when value="single"> 274
307 <expand macro="input_param" /> 275 <tests>
308 <expand macro="group_params" /> 276 <test>
309 </when> 277 <param name="select" value="mzxml_files" />
310 </conditional> 278 <param name="mzxml_files" value="BSA_min_23.mzXML" />
311 <param format="fasta" name="database" type="data" label="FASTA Database" help="" /> 279 <param name="fasta_files" value="bsa.fasta" />
312 <expand macro="advanced_sequences_conditional" /> 280 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
313 <param name="fixed_modifications" label="Fixed Modifications" type="select" multiple="true"> 281 <param name="description_parse_rule" value="&gt;(.*)" />
314 <expand macro="mod_opts" /> 282 <param name="min_unique_pep" value="0" />
315 </param> 283 <param name="fixed_mods" value="Carbamidomethyl (C)" />
316 <expand macro="identification_conditional" /> 284 <param name="var_mods" value="Oxidation (M)" />
317 <expand macro="protein_quantification_conditional" /> 285 <param name="proteases" value="Trypsin/P" />
318 <expand macro="site_quantification_conditional" /> 286 <param name="write_mztab" value="true" />
319 <expand macro="misc_conditional" /> 287 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />
320 </inputs> 288 <output name="evidence" file="single/combined/txt/evidence.txt" />
321 <outputs> 289 <output name="msms" file="single/combined/txt/msms.txt" />
322 <data format="tabular" name="output_protein_groups" label="MaxQuant Protein Groups for ${on_string}"/> 290 <output name="mzTab" file="single/combined/txt/mzTab.mzTab" lines_diff="4"/>
323 <data format="tabular" name="output_peptides" label="MaxQuant Peptides for ${on_string}"/> 291 <output name="allPeptides" file="single/combined/txt/allPeptides.txt" />
324 <data format="tabular" name="output_evidence" label="MaxQuant Evidence for ${on_string}"/> 292 <output name="msmsScans" file="single/combined/txt/msmsScans.txt" />
325 <data format="tabular" name="output_parameters" label="MaxQuant Tabular Parameters for ${on_string}"/> 293 <output name="mzRange" file="single/combined/txt/mzRange.txt" />
326 <data format="tabular" name="output_msms" label="MaxQuant MSMS for ${on_string}"/> 294 <output name="parameters" file="single/combined/txt/parameters.txt" lines_diff="10"/>
327 <data format="tabular" name="output_mqpar" label="MaxQuant Parameters XML for ${on_string}"/> 295 <output name="peptides" file="single/combined/txt/peptides.txt" />
328 </outputs> 296 <output name="peptideSection" file="single/combined/txt/peptideSection.txt" />
329 <help> 297 <output name="proteinGroups" file="single/combined/txt/proteinGroups.txt" />
330 </help> 298 <output name="summary" file="single/combined/txt/summary.txt" />
299 <output name="modificationSpecificPeptides" file="single/combined/txt/modificationSpecificPeptides.txt" />
300 </test>
301 </tests>
302
303 <help><![CDATA[
304 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
305
306 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a very reduced set of search parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too. If possible, this tool should be preferred.
307
308 **Input files**
309
310 - Thermo raw file or mzXML file
311 - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
312 - Optional files:
313 - Tabular file with experimental design template:
314 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Fraction are abitrary strings, Experiment is an integer, PTM is either True or False.
315
316 ::
317
318 Name Fraction Experiment PTM
319 File1 1 E1 False
320 File2 2 E1 False
321 File3 3 E1 False
322 ...
323 ...
324
325 **Parameter Options**
326
327 - Quantification options
328 - label based:
329 - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections
330 - label-free
331
332 **Output files**
333
334 Different output file options are available, most of them are part of the MaxQuant txt directory.
335 ]]></help>
336 <citations>
337 <citation type="bibtex">
338 @article{cox2008maxquant,
339 title={MaxQuant enables high peptide identification rates, individualized
340 ppb-range mass accuracies and proteome-wide protein quantification},
341 author={Cox, J{\"u}rgen and Mann, Matthias},
342 journal={Nature biotechnology},
343 volume={26},
344 number={12},
345 pages={1367},
346 year={2008},
347 publisher={Nature Publishing Group}
348 }
349 </citation>
350 <citation type="bibtex">
351 @article{tyanova2016maxquant,
352 title={The MaxQuant computational platform for mass
353 spectrometry-based shotgun proteomics},
354 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
355 journal={Nature protocols},
356 volume={11},
357 number={12},
358 pages={2301},
359 year={2016},
360 publisher={Nature Publishing Group}
361 }
362 </citation>
363 </citations>
331 </tool> 364 </tool>