Mercurial > repos > urgi-team > gandalfworkflow

comparison Galaxy-Workflow-creation_workflow_gandalf_2.0.ga @ 0:780ad1e582e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author urgi-team
date Thu, 12 Nov 2015 07:38:20 -0500
parents
children 025efd59ddd0
comparison
equal deleted inserted replaced
-1:000000000000 0:780ad1e582e1
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "creation workflow gandalf 2.0",
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": 288,
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": 288,
44 "top": 285
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 "inputs": [
58 {
59 "description": "",
60 "name": "Input Dataset"
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
65 "position": {
66 "left": 288,
67 "top": 370
68 },
69 "tool_errors": null,
70 "tool_id": null,
71 "tool_state": "{\"name\": \"Input Dataset\"}",
72 "tool_version": null,
73 "type": "data_input",
74 "user_outputs": []
75 },
76 "3": {
77 "annotation": "",
78 "id": 3,
79 "input_connections": {
80 "input_file": {
81 "id": 0,
82 "output_name": "output"
83 }
84 },
85 "inputs": [],
86 "name": "mdust",
87 "outputs": [
88 {
89 "name": "output_masked_fasta",
90 "type": "fasta"
91 },
92 {
93 "name": "output_tab",
94 "type": "tabular"
95 },
96 {
97 "name": "output_bed",
98 "type": "bed"
99 }
100 ],
101 "position": {
102 "left": 571,
103 "top": 394
104 },
105 "post_job_actions": {
106 "RenameDatasetActionoutput_bed": {
107 "action_arguments": {
108 "newname": "#{input_file | basename}.bed"
109 },
110 "action_type": "RenameDatasetAction",
111 "output_name": "output_bed"
112 }
113 },
114 "tool_errors": null,
115 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0",
116 "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
117 "tool_version": "1.0",
118 "type": "tool",
119 "user_outputs": []
120 },
121 "4": {
122 "annotation": "",
123 "id": 4,
124 "input_connections": {
125 "fastq_input|fastq_input1": {
126 "id": 1,
127 "output_name": "output"
128 },
129 "fastq_input|fastq_input2": {
130 "id": 2,
131 "output_name": "output"
132 },
133 "reference_source|ref_file": {
134 "id": 0,
135 "output_name": "output"
136 }
137 },
138 "inputs": [],
139 "name": "Map with BWA-MEM",
140 "outputs": [
141 {
142 "name": "bam_output",
143 "type": "bam"
144 }
145 ],
146 "position": {
147 "left": 516,
148 "top": 200
149 },
150 "post_job_actions": {
151 "RenameDatasetActionbam_output": {
152 "action_arguments": {
153 "newname": "#{fastq_input1 | basename}.bam"
154 },
155 "action_type": "RenameDatasetAction",
156 "output_name": "bam_output"
157 }
158 },
159 "tool_errors": null,
160 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1",
161 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
162 "tool_version": "0.4.1",
163 "type": "tool",
164 "user_outputs": []
165 },
166 "5": {
167 "annotation": "",
168 "id": 5,
169 "input_connections": {
170 "input1": {
171 "id": 4,
172 "output_name": "bam_output"
173 }
174 },
175 "inputs": [],
176 "name": "mapQfilter",
177 "outputs": [
178 {
179 "name": "output1",
180 "type": "bam"
181 }
182 ],
183 "position": {
184 "left": 844,
185 "top": 200
186 },
187 "post_job_actions": {
188 "RenameDatasetActionoutput1": {
189 "action_arguments": {
190 "newname": "#{input1 | basename}.filteredbam"
191 },
192 "action_type": "RenameDatasetAction",
193 "output_name": "output1"
194 }
195 },
196 "tool_errors": null,
197 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0",
198 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input1\": \"null\"}",
199 "tool_version": "1.0",
200 "type": "tool",
201 "user_outputs": []
202 },
203 "6": {
204 "annotation": "",
205 "id": 6,
206 "input_connections": {
207 "inputFile": {
208 "id": 5,
209 "output_name": "output1"
210 }
211 },
212 "inputs": [],
213 "name": "MarkDuplicates",
214 "outputs": [
215 {
216 "name": "metrics_file",
217 "type": "txt"
218 },
219 {
220 "name": "outFile",
221 "type": "bam"
222 }
223 ],
224 "position": {
225 "left": 1072,
226 "top": 200
227 },
228 "post_job_actions": {
229 "RenameDatasetActionoutFile": {
230 "action_arguments": {
231 "newname": "#{inputFile | basename}.markedBAM"
232 },
233 "action_type": "RenameDatasetAction",
234 "output_name": "outFile"
235 }
236 },
237 "tool_errors": null,
238 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0",
239 "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
240 "tool_version": "1.126.0",
241 "type": "tool",
242 "user_outputs": []
243 },
244 "7": {
245 "annotation": "",
246 "id": 7,
247 "input_connections": {
248 "input1": {
249 "id": 6,
250 "output_name": "outFile"
251 }
252 },
253 "inputs": [],
254 "name": "flagstat",
255 "outputs": [
256 {
257 "name": "output1",
258 "type": "txt"
259 }
260 ],
261 "position": {
262 "left": 1400,
263 "top": 200
264 },
265 "post_job_actions": {
266 "RenameDatasetActionoutput1": {
267 "action_arguments": {
268 "newname": "#{inupt1| basename}.stats"
269 },
270 "action_type": "RenameDatasetAction",
271 "output_name": "output1"
272 }
273 },
274 "tool_errors": null,
275 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1",
276 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
277 "tool_version": "1.0.0",
278 "type": "tool",
279 "user_outputs": []
280 },
281 "8": {
282 "annotation": "",
283 "id": 8,
284 "input_connections": {
285 "input_bams_0|input_bam": {
286 "id": 6,
287 "output_name": "outFile"
288 },
289 "reference_source|ref_file": {
290 "id": 0,
291 "output_name": "output"
292 }
293 },
294 "inputs": [],
295 "name": "Freebayes4Workflow",
296 "outputs": [
297 {
298 "name": "output_vcf_default",
299 "type": "vcf"
300 },
301 {
302 "name": "output_vcf_firstBAM",
303 "type": "vcf"
304 },
305 {
306 "name": "output_vcf_rename",
307 "type": "vcf"
308 },
309 {
310 "name": "output_failed_alleles_bed",
311 "type": "bed"
312 },
313 {
314 "name": "output_trace",
315 "type": "txt"
316 }
317 ],
318 "position": {
319 "left": 1400,
320 "top": 313
321 },
322 "post_job_actions": {},
323 "tool_errors": null,
324 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5",
325 "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}",
326 "tool_version": "0.5",
327 "type": "tool",
328 "user_outputs": []
329 },
330 "9": {
331 "annotation": "",
332 "id": 9,
333 "input_connections": {
334 "BedFile_List|BedFiles_0|inputBed": {
335 "id": 3,
336 "output_name": "output_bed"
337 },
338 "inputVCF": {
339 "id": 8,
340 "output_name": "output_vcf_firstBAM"
341 }
342 },
343 "inputs": [],
344 "name": "VCFFiltering",
345 "outputs": [
346 {
347 "name": "outputVCF",
348 "type": "vcf"
349 },
350 {
351 "name": "output_html",
352 "type": "html"
353 }
354 ],
355 "position": {
356 "left": 1904,
357 "top": 265
358 },
359 "post_job_actions": {
360 "RenameDatasetActionoutputVCF": {
361 "action_arguments": {
362 "newname": "#{inputVCF | basename}.filteredVCF"
363 },
364 "action_type": "RenameDatasetAction",
365 "output_name": "outputVCF"
366 },
367 "RenameDatasetActionoutput_html": {
368 "action_arguments": {
369 "newname": "#{inputVCF | basename}.VCFFiltering.graphs"
370 },
371 "action_type": "RenameDatasetAction",
372 "output_name": "output_html"
373 }
374 },
375 "tool_errors": null,
376 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01",
377 "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
378 "tool_version": "0.01",
379 "type": "tool",
380 "user_outputs": []
381 }
382 },
383 "uuid": "7ffb6371-3f23-4cfe-8c68-70019963aa4a"
384 }