Mercurial > repos > galaxyp > openms_compnovocid

comparison hardcoded_params.json @ 17:123ea5520652 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:08:54 +0000
parents adcd1571a1c5
children
comparison
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16:adcd1571a1c5 17:123ea5520652
1 {
2 "#": "blacklist parameters",
3
4 "version": [{"value": "@"}],
5 "debug": [{"value": "@"}],
6 "algorithm:debug": [{"value": "@"}],
7 "java_memory": [{"value": "@"}],
8 "java_permgen": [{"value": "@"}],
9 "#": "type of input is always determined from the file extension ",
10 "in_type": [{"value": "@"}],
11
12 "#": "tool specific blacklist parameters",
13
14 "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}],
15 "NET_executable": [{
16 "value": "@",
17 "tools": ["FileConverter"]
18 }],
19
20
21 "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}],
22
23 "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled",
24 "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
25 "#": "TODO would need treatment as prefix-output",
26 "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
27
28 "#": "hardcode parameter values",
29
30 "comet_version": [{
31 "value":"2016.01 rev. 3"
32 }],
33 "comet_executable": [{
34 "value":"comet"
35 }],
36 "crux_executable": [{
37 "value": "crux"
38 }],
39 "fido_executable": [{
40 "value":"Fido"
41 }],
42 "fidocp_executable": [{
43 "value":"FidoChooseParameters"
44 }],
45 "maracluster_executable": [{
46 "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
47 }],
48 "mascot_directory": [{
49 "value":"TODO"
50 }],
51 "myrimatch_executable": [{
52 "value":"myrimatch"
53 }],
54 "omssa_executable": [{
55 "value":"$(dirname $(realpath $(which omssacl)))/omssacl"
56 }],
57 "ThermoRaw_executable": [{
58 "value": "ThermoRawFileParser.exe",
59 "tools": ["FileConverter"]
60 }],
61 "pepnovo_executable": [{
62 "value":"pepnovo"
63 }],
64 "percolator_executable": [{
65 "value":"percolator"
66 }],
67 "xtandem_executable": [{
68 "value":"xtandem"
69 }],
70 "executable": [
71 {
72 "value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar",
73 "tools": ["LuciphorAdapter"]
74 }, {
75 "value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar",
76 "tools": ["MSFraggerAdapter"]
77 }, {
78 "value":"$(msgf_plus -get_jar_path)",
79 "tools": ["MSGFPlusAdapter"]
80 }, {
81 "value": "/home/berntm/Downloads/novor/lib/novor.jar",
82 "tools": ["NovorAdapter"]
83 }, {
84 "value":"$(which sirius)",
85 "tools": ["SiriusAdapter", "AssayGeneratorMetabo"]
86 }, {
87 "value":"spectrast",
88 "tools": ["SpectraSTSearchAdapter"]
89 }
90 ],
91 "r_executable": [{
92 "value":"R"
93 }],
94 "rscript_executable": [{
95 "value":"Rscript"
96 }],
97 "java_executable": [{
98 "value":"java"
99 }],
100 "log": [{
101 "value":"log.txt"
102 }],
103 "tempDirectory": [{
104 "value":"$TMP_DIR"
105 }],
106 "temp_data_directory": [{
107 "value":"$TMP_DIR"
108 }],
109 "algorithm:Preprocessing:tmp_dir": [{
110 "value":"$TMP_DIR"
111 }],
112 "no_progress": [{
113 "value": true
114 }],
115 "#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed",
116 "num_threads": [{
117 "value":"${GALAXY_SLOTS:-1}"
118 }],
119 "threads": [{
120 "value": "${GALAXY_SLOTS:-1}"
121 }],
122 "sirius:cores": [{
123 "value": "${GALAXY_SLOTS:-1}"
124 }],
125
126 "#": "hardcode the outer loop threads for OpenSwathWorkflow",
127 "outer_loop_threads": [{
128 "value": "1",
129 "tools": ["OpenSwathWorkflow"]
130 }],
131 "separator": [{
132 "value": ",",
133 "tools": ["IDMassAccuracy"]
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
142 "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)",
143
144 "#": "test is not a hardcoded value since we need to set it in the tool tests",
145 "test": [{
146 "CTD:type": "text",
147 "XML:type": "hidden"
148 }],
149
150 "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)",
151
152 "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools",
153 "out_type": [{
154 "CTD:required": true,
155 "CTD:advanced": false
156 }],
157
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",
159 "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here",
160 "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404",
161 "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)",
162 "out": [{
163 "CTD:is_list": false,
164 "tools": ["SeedListGenerator"]
165 }, {
166 "CTD:required": true,
167 "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"]
168 }, {
169 "CTD:type": "output-prefix",
170 "CTD:required": true,
171 "CTD:restrictions": "mzml",
172 "tools": ["MzMLSplitter"]
173 }, {
174 "value": "@",
175 "tools": ["IDRipper"]
176 }],
177
178 "#": "Try to remove xml data type whereever possible",
179 "#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
180 "xml_out": [{
181 "CTD:restrictions": "bioml",
182 "tools": ["XTandemAdapter"]
183 }],
184
185 "#": "IDFileConverter remove xml",
186 "#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
187 "#": "XFDR does not need xml .. redundant with xquest.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",
189 "in": [{
190 "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml",
191 "tools": ["IDFileConverter"]
192 }, {
193 "CTD:is_list": false,
194 "tools": ["OpenSwathWorkflow"]
195 }, {
196 "CTD:restrictions": "idXML,mzid,xquest.xml",
197 "tools": ["XFDR"]
198 }, {
199 "CTD:restrictions": "mzML,idXML,featureXML",
200 "tools": ["SeedListGenerator"]
201 }],
202
203 "#": "IDMapper has in and spectra:in params, in is used in out as format_source",
204 "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493",
205 "spectra:in": [{
206 "CTD:name": "_in",
207 "tools": ["IDMapper"]
208 }],
209
210 "#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527",
211 "#": "output-prefix",
212 "out_path": [{
213 "CTD:type": "output-prefix",
214 "CTD:required": true,
215 "CTD:restrictions": "idXML",
216 "tools": ["IDRipper"]
217 }],
218 "outputDirectory": [{
219 "CTD:type": "output-prefix",
220 "CTD:advanced": false,
221 "CTD:required": true,
222 "CTD:restrictions": "mzml",
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
235 }]
236 }