Mercurial > repos > galaxyp > openms_qcembedder
comparison hardcoded_params.json @ 11:2c6f5858e89a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 19:55:08 +0000 |
parents | a717bea32e41 |
children |
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10:a717bea32e41 | 11:2c6f5858e89a |
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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 } |