1
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "",
|
|
4 "format-version": "0.1",
|
|
5 "name": "workflow gandalf 1.0",
|
|
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": 467,
|
|
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": 467,
|
|
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 "inputs": [
|
|
58 {
|
|
59 "description": "",
|
|
60 "name": "Input Dataset"
|
|
61 }
|
|
62 ],
|
|
63 "name": "Input dataset",
|
|
64 "outputs": [],
|
|
65 "position": {
|
|
66 "left": 467,
|
|
67 "top": 440
|
|
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 "fastq_input|fastq_input1": {
|
|
81 "id": 1,
|
|
82 "output_name": "output"
|
|
83 },
|
|
84 "fastq_input|fastq_input2": {
|
|
85 "id": 2,
|
|
86 "output_name": "output"
|
|
87 },
|
|
88 "reference_source|ref_file": {
|
|
89 "id": 0,
|
|
90 "output_name": "output"
|
|
91 }
|
|
92 },
|
|
93 "inputs": [],
|
|
94 "name": "Map with BWA-MEM",
|
|
95 "outputs": [
|
|
96 {
|
|
97 "name": "bam_output",
|
|
98 "type": "bam"
|
|
99 }
|
|
100 ],
|
|
101 "position": {
|
|
102 "left": 661,
|
|
103 "top": 204
|
|
104 },
|
|
105 "post_job_actions": {
|
|
106 "RenameDatasetActionbam_output": {
|
|
107 "action_arguments": {
|
|
108 "newname": "#{fastq_input1 | basename}.bam"
|
|
109 },
|
|
110 "action_type": "RenameDatasetAction",
|
|
111 "output_name": "bam_output"
|
|
112 }
|
|
113 },
|
|
114 "tool_errors": null,
|
|
115 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1",
|
|
116 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"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\\\"\"}",
|
|
117 "tool_version": "0.4.1",
|
|
118 "type": "tool",
|
|
119 "user_outputs": []
|
|
120 },
|
|
121 "4": {
|
|
122 "annotation": "",
|
|
123 "id": 4,
|
|
124 "input_connections": {
|
|
125 "input1": {
|
|
126 "id": 3,
|
|
127 "output_name": "bam_output"
|
|
128 }
|
|
129 },
|
|
130 "inputs": [],
|
|
131 "name": "mapQfilter",
|
|
132 "outputs": [
|
|
133 {
|
|
134 "name": "output1",
|
|
135 "type": "bam"
|
|
136 }
|
|
137 ],
|
|
138 "position": {
|
|
139 "left": 944,
|
|
140 "top": 161
|
|
141 },
|
|
142 "post_job_actions": {
|
|
143 "RenameDatasetActionoutput1": {
|
|
144 "action_arguments": {
|
|
145 "newname": "#{input1 | basename}.bam"
|
|
146 },
|
|
147 "action_type": "RenameDatasetAction",
|
|
148 "output_name": "output1"
|
|
149 }
|
|
150 },
|
|
151 "tool_errors": null,
|
|
152 "tool_id": "10.0.0.125:9009/repos/urgiteam/mapqfilter/mapQfilter/1.0",
|
|
153 "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\"}",
|
|
154 "tool_version": "1.0",
|
|
155 "type": "tool",
|
|
156 "user_outputs": []
|
|
157 },
|
|
158 "5": {
|
|
159 "annotation": "",
|
|
160 "id": 5,
|
|
161 "input_connections": {
|
|
162 "inputFile": {
|
|
163 "id": 4,
|
|
164 "output_name": "output1"
|
|
165 }
|
|
166 },
|
|
167 "inputs": [],
|
|
168 "name": "MarkDuplicates",
|
|
169 "outputs": [
|
|
170 {
|
|
171 "name": "metrics_file",
|
|
172 "type": "txt"
|
|
173 },
|
|
174 {
|
|
175 "name": "outFile",
|
|
176 "type": "bam"
|
|
177 }
|
|
178 ],
|
|
179 "position": {
|
|
180 "left": 1121,
|
|
181 "top": 208
|
|
182 },
|
|
183 "post_job_actions": {
|
|
184 "RenameDatasetActionoutFile": {
|
|
185 "action_arguments": {
|
|
186 "newname": "#{inputFile | basename}.markedBAM"
|
|
187 },
|
|
188 "action_type": "RenameDatasetAction",
|
|
189 "output_name": "outFile"
|
|
190 }
|
|
191 },
|
|
192 "tool_errors": null,
|
|
193 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0",
|
|
194 "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\"}",
|
|
195 "tool_version": "1.126.0",
|
|
196 "type": "tool",
|
|
197 "user_outputs": []
|
|
198 },
|
|
199 "6": {
|
|
200 "annotation": "",
|
|
201 "id": 6,
|
|
202 "input_connections": {
|
|
203 "input_bams_0|input_bam": {
|
|
204 "id": 5,
|
|
205 "output_name": "outFile"
|
|
206 },
|
|
207 "reference_source|ref_file": {
|
|
208 "id": 0,
|
|
209 "output_name": "output"
|
|
210 }
|
|
211 },
|
|
212 "inputs": [],
|
|
213 "name": "FreeBayesFix",
|
|
214 "outputs": [
|
|
215 {
|
|
216 "name": "output_vcf_default",
|
|
217 "type": "vcf"
|
|
218 },
|
|
219 {
|
|
220 "name": "output_vcf_firstBAM",
|
|
221 "type": "vcf"
|
|
222 },
|
|
223 {
|
|
224 "name": "output_vcf_rename",
|
|
225 "type": "vcf"
|
|
226 },
|
|
227 {
|
|
228 "name": "output_failed_alleles_bed",
|
|
229 "type": "bed"
|
|
230 },
|
|
231 {
|
|
232 "name": "output_trace",
|
|
233 "type": "txt"
|
|
234 }
|
|
235 ],
|
|
236 "position": {
|
|
237 "left": 1347,
|
|
238 "top": 320
|
|
239 },
|
|
240 "post_job_actions": {},
|
|
241 "tool_errors": null,
|
|
242 "tool_id": "10.0.0.125:9009/repos/urgiteam/freebayes/freebayes-fix/0.4",
|
|
243 "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}\"}",
|
|
244 "tool_version": "0.4",
|
|
245 "type": "tool",
|
|
246 "user_outputs": []
|
|
247 },
|
|
248 "7": {
|
|
249 "annotation": "",
|
|
250 "id": 7,
|
|
251 "input_connections": {
|
|
252 "input1": {
|
|
253 "id": 5,
|
|
254 "output_name": "outFile"
|
|
255 }
|
|
256 },
|
|
257 "inputs": [],
|
|
258 "name": "flagstat",
|
|
259 "outputs": [
|
|
260 {
|
|
261 "name": "output1",
|
|
262 "type": "txt"
|
|
263 }
|
|
264 ],
|
|
265 "position": {
|
|
266 "left": 1395,
|
|
267 "top": 208
|
|
268 },
|
|
269 "post_job_actions": {},
|
|
270 "tool_errors": null,
|
|
271 "tool_id": "samtools_flagstat",
|
|
272 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
273 "tool_version": "1.0.0",
|
|
274 "type": "tool",
|
|
275 "user_outputs": []
|
|
276 },
|
|
277 "8": {
|
|
278 "annotation": "",
|
|
279 "id": 8,
|
|
280 "input_connections": {
|
|
281 "inputVCF": {
|
|
282 "id": 6,
|
|
283 "output_name": "output_vcf_firstBAM"
|
|
284 }
|
|
285 },
|
|
286 "inputs": [],
|
|
287 "name": "VCFFiltering",
|
|
288 "outputs": [
|
|
289 {
|
|
290 "name": "outputVCF",
|
|
291 "type": "vcf"
|
|
292 },
|
|
293 {
|
|
294 "name": "output_html",
|
|
295 "type": "html"
|
|
296 }
|
|
297 ],
|
|
298 "position": {
|
|
299 "left": 1714,
|
|
300 "top": 180
|
|
301 },
|
|
302 "post_job_actions": {
|
|
303 "RenameDatasetActionoutputVCF": {
|
|
304 "action_arguments": {
|
|
305 "newname": "#{inputVCF | basename}.filteredVCF"
|
|
306 },
|
|
307 "action_type": "RenameDatasetAction",
|
|
308 "output_name": "outputVCF"
|
|
309 }
|
|
310 },
|
|
311 "tool_errors": null,
|
|
312 "tool_id": "10.0.0.125:9009/repos/urgiteam/vcfgandalftools/VCFFiltering/0.01",
|
|
313 "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"is_BedFile\\\": \\\"False\\\", \\\"__current_case__\\\": 0}\", \"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\\\"\"}",
|
|
314 "tool_version": "0.01",
|
|
315 "type": "tool",
|
|
316 "user_outputs": []
|
|
317 }
|
|
318 },
|
|
319 "uuid": "1a7a40af-5624-4049-a1dd-fee31e8731ee"
|
|
320 } |