|
0
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "PRIMS- (iTRAQ) labeled data",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "id": 0,
|
|
|
10 "input_connections": {},
|
|
|
11 "inputs": [
|
|
|
12 {
|
|
|
13 "description": "",
|
|
|
14 "name": "Input Dataset"
|
|
|
15 }
|
|
|
16 ],
|
|
|
17 "name": "Input dataset",
|
|
|
18 "outputs": [],
|
|
|
19 "position": {
|
|
|
20 "left": 200,
|
|
|
21 "top": 200
|
|
|
22 },
|
|
|
23 "tool_errors": null,
|
|
|
24 "tool_id": null,
|
|
|
25 "tool_state": "{\"name\": \"Input Dataset\"}",
|
|
|
26 "tool_version": null,
|
|
|
27 "type": "data_input",
|
|
|
28 "user_outputs": []
|
|
|
29 },
|
|
|
30 "1": {
|
|
|
31 "annotation": "",
|
|
|
32 "id": 1,
|
|
|
33 "input_connections": {},
|
|
|
34 "inputs": [
|
|
|
35 {
|
|
|
36 "description": "",
|
|
|
37 "name": "Input Dataset"
|
|
|
38 }
|
|
|
39 ],
|
|
|
40 "name": "Input dataset",
|
|
|
41 "outputs": [],
|
|
|
42 "position": {
|
|
|
43 "left": 200,
|
|
|
44 "top": 320
|
|
|
45 },
|
|
|
46 "tool_errors": null,
|
|
|
47 "tool_id": null,
|
|
|
48 "tool_state": "{\"name\": \"Input Dataset\"}",
|
|
|
49 "tool_version": null,
|
|
|
50 "type": "data_input",
|
|
|
51 "user_outputs": []
|
|
|
52 },
|
|
|
53 "2": {
|
|
|
54 "annotation": "",
|
|
|
55 "id": 2,
|
|
|
56 "input_connections": {
|
|
|
57 "database": {
|
|
|
58 "id": 0,
|
|
|
59 "output_name": "output"
|
|
|
60 },
|
|
|
61 "fileType|inputFile": {
|
|
|
62 "id": 1,
|
|
|
63 "output_name": "output"
|
|
|
64 }
|
|
|
65 },
|
|
|
66 "inputs": [
|
|
|
67 {
|
|
|
68 "description": "runtime parameter for tool X!Tandem",
|
|
|
69 "name": "precursor_mass_tolerance_lower"
|
|
|
70 },
|
|
|
71 {
|
|
|
72 "description": "runtime parameter for tool X!Tandem",
|
|
|
73 "name": "precursor_mass_tolerance_upper"
|
|
|
74 },
|
|
|
75 {
|
|
|
76 "description": "runtime parameter for tool X!Tandem",
|
|
|
77 "name": "precursor_error_units"
|
|
|
78 }
|
|
|
79 ],
|
|
|
80 "name": "X!Tandem",
|
|
|
81 "outputs": [
|
|
|
82 {
|
|
|
83 "name": "outputFile",
|
|
|
84 "type": "bioml"
|
|
|
85 },
|
|
|
86 {
|
|
|
87 "name": "htmlReportFile",
|
|
|
88 "type": "html"
|
|
|
89 },
|
|
|
90 {
|
|
|
91 "name": "outTsv",
|
|
|
92 "type": "tabular"
|
|
|
93 }
|
|
|
94 ],
|
|
|
95 "position": {
|
|
|
96 "left": 422,
|
|
|
97 "top": 199
|
|
|
98 },
|
|
|
99 "post_job_actions": {},
|
|
|
100 "tool_errors": null,
|
|
|
101 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_xtandem200/2.0.0",
|
|
|
102 "tool_state": "{\"__page__\": 0, \"fragment_error_units\": \"\\\"Daltons\\\"\", \"precursor_mass_tolerance_lower\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"database\": \"null\", \"minimum_fragment_mz\": \"\\\"150\\\"\", \"fileType\": \"{\\\"type\\\": \\\"fileSet\\\", \\\"__current_case__\\\": 1, \\\"inputFile\\\": null}\", \"potential_modifications\": \"[\\\"45.987721@C\\\", \\\"144.102063@[\\\", \\\"144.102063@K\\\"]\", \"cleavage_site\": \"\\\"[RK]|{P}\\\"\", \"maximum_missed_cleavage_sites\": \"\\\"1\\\"\", \"fixed_modifications\": \"\\\"45.987721@C,144.102063@[,144.102063@K\\\"\", \"refinementOpt\": \"{\\\"refinement\\\": \\\"yes\\\", \\\"refine_potential_modifications\\\": null, \\\"refine_max_valid_expect\\\": \\\"0.01\\\", \\\"__current_case__\\\": 0, \\\"refine_point_mutation\\\": \\\"yes\\\"}\", \"max_valid_expect\": \"\\\"0.1\\\"\", \"precursor_mass_tolerance_upper\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragment_mass_tolerance\": \"\\\"0.6\\\"\", \"precursor_error_units\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reverse_scoring\": \"\\\"no\\\"\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
|
|
|
103 "tool_version": "2.0.0",
|
|
|
104 "type": "tool",
|
|
|
105 "user_outputs": []
|
|
|
106 },
|
|
|
107 "3": {
|
|
|
108 "annotation": "",
|
|
|
109 "id": 3,
|
|
|
110 "input_connections": {
|
|
|
111 "fileType|inputFormatType|inputFile": {
|
|
|
112 "id": 2,
|
|
|
113 "output_name": "outputFile"
|
|
|
114 }
|
|
|
115 },
|
|
|
116 "inputs": [],
|
|
|
117 "name": "DB search converter",
|
|
|
118 "outputs": [
|
|
|
119 {
|
|
|
120 "name": "outputFile",
|
|
|
121 "type": "mzid"
|
|
|
122 }
|
|
|
123 ],
|
|
|
124 "position": {
|
|
|
125 "left": 640,
|
|
|
126 "top": 200
|
|
|
127 },
|
|
|
128 "post_job_actions": {},
|
|
|
129 "tool_errors": null,
|
|
|
130 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/masscomb_dbsearch_converter/1.0.1",
|
|
|
131 "tool_state": "{\"__page__\": 0, \"fileType\": \"{\\\"inputFormatType\\\": {\\\"isMs2SpectrumIdStartingAtZero\\\": \\\"true\\\", \\\"inputFormat\\\": \\\"xtandem\\\", \\\"__current_case__\\\": 0, \\\"inputFile\\\": null}, \\\"type\\\": \\\"fileSet\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
|
|
|
132 "tool_version": "1.0.1",
|
|
|
133 "type": "tool",
|
|
|
134 "user_outputs": []
|
|
|
135 },
|
|
|
136 "4": {
|
|
|
137 "annotation": "",
|
|
|
138 "id": 4,
|
|
|
139 "input_connections": {
|
|
|
140 "ppidsFileName": {
|
|
|
141 "id": 3,
|
|
|
142 "output_name": "outputFile"
|
|
|
143 },
|
|
|
144 "spectraDataFile": {
|
|
|
145 "id": 1,
|
|
|
146 "output_name": "output"
|
|
|
147 }
|
|
|
148 },
|
|
|
149 "inputs": [],
|
|
|
150 "name": "Quantiline",
|
|
|
151 "outputs": [
|
|
|
152 {
|
|
|
153 "name": "outputFile",
|
|
|
154 "type": "apml"
|
|
|
155 },
|
|
|
156 {
|
|
|
157 "name": "outReport",
|
|
|
158 "type": "html"
|
|
|
159 }
|
|
|
160 ],
|
|
|
161 "position": {
|
|
|
162 "left": 860,
|
|
|
163 "top": 200
|
|
|
164 },
|
|
|
165 "post_job_actions": {},
|
|
|
166 "tool_errors": null,
|
|
|
167 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantiline1/1.0.2",
|
|
|
168 "tool_state": "{\"ppidsFileName\": \"null\", \"__page__\": 0, \"labelMzValues\": \"\\\"114.0,115.0,116.0,117.0\\\"\", \"__rerun_remap_job_id__\": null, \"spectraDataFile\": \"null\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"labelmTol\": \"\\\"0.5\\\"\"}",
|
|
|
169 "tool_version": "1.0.2",
|
|
|
170 "type": "tool",
|
|
|
171 "user_outputs": []
|
|
|
172 },
|
|
|
173 "5": {
|
|
|
174 "annotation": "",
|
|
|
175 "id": 5,
|
|
|
176 "input_connections": {
|
|
|
177 "annotationSourceFiles_0|identificationsFile": {
|
|
|
178 "id": 3,
|
|
|
179 "output_name": "outputFile"
|
|
|
180 },
|
|
|
181 "annotationSourceFiles_0|spectraFile": {
|
|
|
182 "id": 1,
|
|
|
183 "output_name": "output"
|
|
|
184 },
|
|
|
185 "apmlFile": {
|
|
|
186 "id": 4,
|
|
|
187 "output_name": "outputFile"
|
|
|
188 }
|
|
|
189 },
|
|
|
190 "inputs": [],
|
|
|
191 "name": "MsFilt",
|
|
|
192 "outputs": [
|
|
|
193 {
|
|
|
194 "name": "outputApml",
|
|
|
195 "type": "apml"
|
|
|
196 },
|
|
|
197 {
|
|
|
198 "name": "outNewIdsApml",
|
|
|
199 "type": "apml"
|
|
|
200 },
|
|
|
201 {
|
|
|
202 "name": "outputCSV",
|
|
|
203 "type": "csv"
|
|
|
204 },
|
|
|
205 {
|
|
|
206 "name": "outRankingTable",
|
|
|
207 "type": "csv"
|
|
|
208 },
|
|
|
209 {
|
|
|
210 "name": "outProteinCoverageCSV",
|
|
|
211 "type": "csv"
|
|
|
212 },
|
|
|
213 {
|
|
|
214 "name": "htmlReportFile",
|
|
|
215 "type": "html"
|
|
|
216 }
|
|
|
217 ],
|
|
|
218 "position": {
|
|
|
219 "left": 1080,
|
|
|
220 "top": 200
|
|
|
221 },
|
|
|
222 "post_job_actions": {},
|
|
|
223 "tool_errors": null,
|
|
|
224 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/msfilt/1.0.2",
|
|
|
225 "tool_state": "{\"annotationSourceFiles\": \"[{\\\"identificationsFile\\\": null, \\\"__index__\\\": 0, \\\"spectraFile\\\": null}]\", \"filterOutFPIds\": \"\\\"True\\\"\", \"filterOutFPAnnotations\": \"\\\"True\\\"\", \"addRawIntensityInfo\": \"\\\"False\\\"\", \"addScaledIntensityInfo\": \"\\\"False\\\"\", \"__page__\": 0, \"apmlFile\": \"null\", \"fpCriteriaExpression\": \"\\\"qmDRT <0 or qmDMA <-0.5 or (qmDMP <-0.5 and qmBSCR<-0.5) or (!isNaN(smXTD) and smXTD >0.01)\\\"\", \"statisticalMeasuresConfig\": \"\\\"smXTD => MS:1001330,XSLASH!Tandem:expect,min \\\\r\\\\npvCSVEX => p_value,CSV_EXPORT,min \\\\r\\\\nsmAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max \\\\r\\\\nsmLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max \\\"\", \"rankingWeightConfig\": \"\\\"qmDRT => delta rt (standard score),1 \\\\r\\\\nqmDMA => delta mass annotation (standard score),1 \\\\r\\\\nqmDMP => delta mass psm (standard score),1 \\\\r\\\\nqmBSCR => best peptide score (standard score),1 \\\\r\\\\nqmALCV => alignment coverage (fraction),1 \\\\r\\\\nqmSTCV => score type coverage (fraction),1 \\\\r\\\\nqmPACV => peptide's best proteinAnnotCoverage (standard score),1 \\\\r\\\\nqmPICV => peptide's best proteinIdentifCoverage (standard score),1 \\\\r\\\\nqmANS => annotation sources (count),1 \\\\r\\\\nqmCSEV => charge states evidence (count),0.2 \\\\r\\\\nqmBCSP=> best correlation with source or product peptide (correl),1 \\\\r\\\\nqmBCCS => best correlation with other charge state (correl),1 \\\\r\\\\nqmBCOS => best correlation with other sibling peptide (correl),1 \\\"\", \"addRawRankingInfo\": \"\\\"False\\\"\", \"fpCriteriaExpressionForIds\": \"\\\"(qmDMP <-0.5 and qmBSCR<-0.5) or (!isNaN(smXTD) and smXTD >0.01)\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"filterOutUnannotatedAlignments\": \"\\\"True\\\"\"}",
|
|
|
226 "tool_version": "1.0.2",
|
|
|
227 "type": "tool",
|
|
|
228 "user_outputs": []
|
|
|
229 },
|
|
|
230 "6": {
|
|
|
231 "annotation": "",
|
|
|
232 "id": 6,
|
|
|
233 "input_connections": {
|
|
|
234 "annotatedQuantificationFiles_0|annotatedQuantificationFile": {
|
|
|
235 "id": 5,
|
|
|
236 "output_name": "outputApml"
|
|
|
237 },
|
|
|
238 "identificationFiles_0|identificationFile": {
|
|
|
239 "id": 5,
|
|
|
240 "output_name": "outNewIdsApml"
|
|
|
241 }
|
|
|
242 },
|
|
|
243 "inputs": [],
|
|
|
244 "name": "Quantifere",
|
|
|
245 "outputs": [
|
|
|
246 {
|
|
|
247 "name": "outputCSV",
|
|
|
248 "type": "csv"
|
|
|
249 },
|
|
|
250 {
|
|
|
251 "name": "outputInferenceLogCSV",
|
|
|
252 "type": "csv"
|
|
|
253 },
|
|
|
254 {
|
|
|
255 "name": "htmlReportFile",
|
|
|
256 "type": "html"
|
|
|
257 },
|
|
|
258 {
|
|
|
259 "name": "outputSummaryAnnotationCSV",
|
|
|
260 "type": "csv"
|
|
|
261 }
|
|
|
262 ],
|
|
|
263 "position": {
|
|
|
264 "left": 1300,
|
|
|
265 "top": 200
|
|
|
266 },
|
|
|
267 "post_job_actions": {},
|
|
|
268 "tool_errors": null,
|
|
|
269 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_proteomics/quantifere1/1.0.2",
|
|
|
270 "tool_state": "{\"__page__\": 0, \"identificationFiles\": \"[{\\\"__index__\\\": 0, \\\"identificationFile\\\": null}]\", \"quantificationDataToUse\": \"\\\"auto\\\"\", \"minAboveAverageHits\": \"\\\"1\\\"\", \"statisticalMeasuresConfig\": \"\\\"smXTD => MS:1001330,XSLASH!Tandem:expect,min \\\\r\\\\npvCSVEX => p_value,CSV_EXPORT,min \\\\r\\\\nsmAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max \\\\r\\\\nsmLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max \\\"\", \"annotatedQuantificationFiles\": \"[{\\\"__index__\\\": 0, \\\"annotatedQuantificationFile\\\": null}]\", \"refineModel\": \"\\\"True\\\"\", \"minProtCoverage\": \"\\\"5.0\\\"\", \"minNrIdsForInferencePeptide\": \"\\\"1\\\"\", \"functionalAnnotationCSV\": \"null\", \"minCorrel\": \"\\\"0.85\\\"\", \"summaryReport\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"is2D_LC_MS\": \"{\\\"fractions\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}",
|
|
|
271 "tool_version": "1.0.2",
|
|
|
272 "type": "tool",
|
|
|
273 "user_outputs": []
|
|
|
274 },
|
|
|
275 "7": {
|
|
|
276 "annotation": "",
|
|
|
277 "id": 7,
|
|
|
278 "input_connections": {
|
|
|
279 "csvDataFile": {
|
|
|
280 "id": 6,
|
|
|
281 "output_name": "outputInferenceLogCSV"
|
|
|
282 }
|
|
|
283 },
|
|
|
284 "inputs": [],
|
|
|
285 "name": "CytoExport",
|
|
|
286 "outputs": [
|
|
|
287 {
|
|
|
288 "name": "htmlReportFile",
|
|
|
289 "type": "html"
|
|
|
290 },
|
|
|
291 {
|
|
|
292 "name": "cysOutFile",
|
|
|
293 "type": "cys"
|
|
|
294 },
|
|
|
295 {
|
|
|
296 "name": "logFile",
|
|
|
297 "type": "txt"
|
|
|
298 }
|
|
|
299 ],
|
|
|
300 "position": {
|
|
|
301 "left": 1520,
|
|
|
302 "top": 200
|
|
|
303 },
|
|
|
304 "post_job_actions": {},
|
|
|
305 "tool_errors": null,
|
|
|
306 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/primv_visualization/cytoexport1/1.0.2",
|
|
|
307 "tool_state": "{\"__page__\": 0, \"csvDataFile\": \"null\", \"__rerun_remap_job_id__\": null, \"configInputMode\": \"{\\\"vizMapPropsFile\\\": \\\"/com/pri/cytoexport/resources/quantifere_network_layout.props\\\", \\\"type\\\": \\\"existingTemplate\\\", \\\"alternativeTableImportJsonFile\\\": \\\"/com/pri/cytoexport/resources/quantifere_network_config.json\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/lukas007/galaxy-test/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"vizStyleName\": \"\\\"default\\\"\"}",
|
|
|
308 "tool_version": "1.0.2",
|
|
|
309 "type": "tool",
|
|
|
310 "user_outputs": []
|
|
|
311 }
|
|
|
312 }
|
|
|
313 } |
