Mercurial > repos > galaxyp > openms_compnovo

comparison hardcoded_params.json @ 14:3a8e53c6b9d6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:07:13 +0000
parents ef622c891b92
children
comparison
equal deleted inserted replaced
13:ef622c891b92 14:3a8e53c6b9d6
117 "value":"${GALAXY_SLOTS:-1}" 117 "value":"${GALAXY_SLOTS:-1}"
118 }], 118 }],
119 "threads": [{ 119 "threads": [{
120 "value": "${GALAXY_SLOTS:-1}" 120 "value": "${GALAXY_SLOTS:-1}"
121 }], 121 }],
122 "sirius:cores": [{
123 "value": "${GALAXY_SLOTS:-1}"
124 }],
125
122 "#": "hardcode the outer loop threads for OpenSwathWorkflow", 126 "#": "hardcode the outer loop threads for OpenSwathWorkflow",
123 "outer_loop_threads": [{ 127 "outer_loop_threads": [{
124 "value": "1", 128 "value": "1",
125 "tools": ["OpenSwathWorkflow"] 129 "tools": ["OpenSwathWorkflow"]
126 }], 130 }],
127 "separator": [{ 131 "separator": [{
128 "value": ",", 132 "value": ",",
129 "tools": ["IDMassAccuracy"] 133 "tools": ["IDMassAccuracy"]
130 }], 134 }],
135
136 "#": "don't alow to copy data internally to save computation time for reloading",
137 "copy_data": [{
138 "value": "false",
139 "tools": ["MapAlignerTreeGuided"]
140 }],
141
131 "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)", 142 "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)",
132 143
133 "#": "test is not a hardcoded value since we need to set it in the tool tests", 144 "#": "test is not a hardcoded value since we need to set it in the tool tests",
134 "test": [{ 145 "test": [{
135 "CTD:type": "text", 146 "CTD:type": "text",
144 "CTD:advanced": false 155 "CTD:advanced": false
145 }], 156 }],
146 157
147 "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter", 158 "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter",
148 "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here", 159 "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here",
149 "#": "MascotAdapter: https://github.com/OpenMS/OpenMS/pull/4553",
150 "#": "Phosphoscoring: https://github.com/OpenMS/OpenMS/pull/4569",
151 "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", 160 "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404",
152 "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", 161 "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)",
153 "out": [{ 162 "out": [{
154 "CTD:is_list": false, 163 "CTD:is_list": false,
155 "tools": ["SeedListGenerator"] 164 "tools": ["SeedListGenerator"]
156 }, { 165 }, {
157 "CTD:required": true, 166 "CTD:required": true,
158 "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] 167 "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"]
159 }, { 168 }, {
160 "CTD:restrictions": "idXML",
161 "tools": ["MascotAdapter"]
162 }, {
163 "CTD:restrictions": "idXML",
164 "tools": ["PhosphoScoring"]
165 }, {
166 "CTD:type": "output-prefix", 169 "CTD:type": "output-prefix",
167 "CTD:required": true, 170 "CTD:required": true,
168 "CTD:restrictions": "mzml", 171 "CTD:restrictions": "mzml",
169 "tools": ["MzMLSplitter"] 172 "tools": ["MzMLSplitter"]
170 }, { 173 }, {
171 "value": "@", 174 "value": "@",
172 "tools": ["IDRipper"] 175 "tools": ["IDRipper"]
173 }], 176 }],
174 177
175 "#": "https://github.com/OpenMS/OpenMS/pull/4552 .. if this is removed the test will need out_cm_FLAG",
176 "out_cm": [{
177 "CTD:required": true,
178 "tools": ["MetaboliteAdductDecharger"]
179 }],
180
181
182 "#": "https://github.com/OpenMS/OpenMS/pull/4451",
183 "out_xquestxml": [{
184 "CTD:restrictions": "xquest.xml",
185 "tools": ["OpenPepXL", "OpenPepXLLF"]
186 }],
187 "out_xquest_specxml": [{
188 "CTD:restrictions": "spec.xml",
189 "tools": ["OpenPepXL", "OpenPepXLLF"]
190 }],
191
192 "#": "Try to remove xml data type whereever possible", 178 "#": "Try to remove xml data type whereever possible",
193 "#": "XTandem Adapter output is called .xml in OMS -> use Galaxy's bioml", 179 "#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
194 "xml_out": [{ 180 "xml_out": [{
195 "CTD:restrictions": "bioml", 181 "CTD:restrictions": "bioml",
196 "tools": ["XTandemAdapter"] 182 "tools": ["XTandemAdapter"]
197 }], 183 }],
198 184
199 "#": "IDFileConverter remove xml", 185 "#": "IDFileConverter remove xml",
200 "#": "OpenSwathWorkflow make in single file input and all outputs non-optional", 186 "#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
201 "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release", 187 "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release",
202 "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", 188 "#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
203 "#": "SeedListGenerator https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
204 "in": [{ 189 "in": [{
205 "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml", 190 "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml",
206 "tools": ["IDFileConverter"] 191 "tools": ["IDFileConverter"]
207 }, { 192 }, {
208 "CTD:is_list": false, 193 "CTD:is_list": false,
209 "tools": ["OpenSwathWorkflow"] 194 "tools": ["OpenSwathWorkflow"]
210 }, { 195 }, {
211 "CTD:restrictions": "idXML,mzid,xquest.xml", 196 "CTD:restrictions": "idXML,mzid,xquest.xml",
212 "tools": ["XFDR"] 197 "tools": ["XFDR"]
213 }, { 198 }, {
214 "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
215 "tools": ["SpectraSTSearchAdapter"]
216 }, {
217 "CTD:restrictions": "mzML,idXML,featureXML", 199 "CTD:restrictions": "mzML,idXML,featureXML",
218 "tools": ["SeedListGenerator"] 200 "tools": ["SeedListGenerator"]
219 }],
220
221 "#": "parameter is a flag but restrictions in wrong order: TODO https://github.com/OpenMS/OpenMS/pull/4455",
222 "# masstrace_snr_filtering": [{
223 "CTD:restrictions": "true,false",
224 "tools": ["MassTraceExtractor"]
225 }], 201 }],
226 202
227 "#": "IDMapper has in and spectra:in params, in is used in out as format_source", 203 "#": "IDMapper has in and spectra:in params, in is used in out as format_source",
228 "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", 204 "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493",
229 "spectra:in": [{ 205 "spectra:in": [{
230 "CTD:name": "_in", 206 "CTD:name": "_in",
231 "tools": ["IDMapper"] 207 "tools": ["IDMapper"]
232 }], 208 }],
233 209
210 "#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527",
234 "#": "output-prefix", 211 "#": "output-prefix",
235 "out_path": [{ 212 "out_path": [{
236 "CTD:type": "output-prefix", 213 "CTD:type": "output-prefix",
237 "CTD:required": true, 214 "CTD:required": true,
238 "CTD:restrictions": "idXML", 215 "CTD:restrictions": "idXML",
242 "CTD:type": "output-prefix", 219 "CTD:type": "output-prefix",
243 "CTD:advanced": false, 220 "CTD:advanced": false,
244 "CTD:required": true, 221 "CTD:required": true,
245 "CTD:restrictions": "mzml", 222 "CTD:restrictions": "mzml",
246 "tools": ["OpenSwathFileSplitter"] 223 "tools": ["OpenSwathFileSplitter"]
224 }],
225
226 "#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443",
227 "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
228 "output_files": [{
229 "CTD:required": true,
230 "tools": ["OpenSwathDIAPreScoring"]
231 }, {
232 "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
233 "tools": ["SpectraSTSearchAdapter"]
234
247 }] 235 }]
248 } 236 }