Mercurial > repos > galaxyp > openms_openpepxllf

comparison hardcoded_params.json @ 4:04168c0bdfa7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:05:58 +0000
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children a8c028751a74
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3:4581cc5b456f 4:04168c0bdfa7
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 "#": "hardcode the outer loop threads for OpenSwathWorkflow",
123 "outer_loop_threads": [{
124 "value": "1",
125 "tools": ["OpenSwathWorkflow"]
126 }],
127 "separator": [{
128 "value": ",",
129 "tools": ["IDMassAccuracy"]
130 }],
131 "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)",
132
133 "#": "test is not a hardcoded value since we need to set it in the tool tests",
134 "test": [{
135 "CTD:type": "text",
136 "XML:type": "hidden"
137 }],
138
139 "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)",
140
141 "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools",
142 "out_type": [{
143 "CTD:required": true,
144 "CTD:advanced": false
145 }],
146
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",
148 "#": "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",
152 "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)",
153 "out": [{
154 "CTD:is_list": false,
155 "tools": ["SeedListGenerator"]
156 }, {
157 "CTD:required": true,
158 "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"]
159 }, {
160 "CTD:restrictions": "idXML",
161 "tools": ["MascotAdapter"]
162 }, {
163 "CTD:restrictions": "idXML",
164 "tools": ["PhosphoScoring"]
165 }, {
166 "CTD:type": "output-prefix",
167 "CTD:required": "true",
168 "CTD:restrictions": "mzml",
169 "tools": ["MzMLSplitter"]
170 }, {
171 "value": "@",
172 "tools": ["IDRipper"]
173 }],
174
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",
193 "#": "XTandem Adapter output is called .xml in OMS -> use Galaxy's bioml",
194 "xml_out": [{
195 "CTD:restrictions": "bioml",
196 "tools": ["XTandemAdapter"]
197 }],
198
199 "#": "IDFileConverter remove xml",
200 "#": "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",
202 "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
203 "#": "SeedListGenerator https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
204 "in": [{
205 "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml",
206 "tools": ["IDFileConverter"]
207 }, {
208 "CTD:is_list": false,
209 "tools": ["OpenSwathWorkflow"]
210 }, {
211 "CTD:restrictions": "idXML,mzid,xquest.xml",
212 "tools": ["XFDR"]
213 }, {
214 "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
215 "tools": ["SpectraSTSearchAdapter"]
216 }, {
217 "CTD:restrictions": "mzML,idXML,featureXML",
218 "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 }],
226
227 "#": "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",
229 "spectra:in": [{
230 "CTD:name": "_in",
231 "tools": ["IDMapper"]
232 }],
233
234 "#": "output-prefix",
235 "out_path": [{
236 "CTD:type": "output-prefix",
237 "CTD:required": "true",
238 "CTD:restrictions": "idXML",
239 "tools": ["IDRipper"]
240 }],
241 "outputDirectory": [{
242 "CTD:type": "output-prefix",
243 "CTD:required": "true",
244 "CTD:restrictions": "mzml",
245 "tools": ["OpenSwathFileSplitter"]
246 }]
247 }