Mercurial > repos > galaxyp > maxquant
comparison maxquant.xml @ 1:8bac3cc5c5de draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author | galaxyp |
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date | Sat, 20 Jul 2019 05:01:05 -0400 |
parents | d4b6c9eae635 |
children | 175e062b6a17 |
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0:d4b6c9eae635 | 1:8bac3cc5c5de |
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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='$msms' |
104 <add value="<"/> | 72 --parameters='$parameters' |
105 <add value=">"/> | 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="^>.*\|(.*)\|.*$"> |
149 <param name="do_mass_filtering" type="boolean" label="Individual Peptide Mass Tolerances" checked="true" truevalue="true" falsevalue="false" /> | 117 <sanitizer> |
150 <param name="max_charge" type="integer" label="Maximum Charge" value="7" /> | 118 <valid initial="string.printable"> |
151 <!-- | 119 <remove value="'"/> |
152 TODO: First charge protease, first charge mods. | 120 </valid> |
153 --> | 121 </sanitizer> |
154 </when> | 122 </param> |
155 </conditional> | 123 <param name="description_parse_rule" type="text" |
156 </macro> | 124 label="description parse rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" |
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="'"/> |
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=">([^\s]*)" /> |
313 <param name="fixed_modifications" label="Fixed Modifications" type="select" multiple="true"> | 281 <param name="description_parse_rule" value=">(.*)" /> |
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> |