comparison Galaxy-Workflow-Phenix_workflow.ga @ 16:55bfe9d1888e draft

Uploaded
author ulfschaefer
date Tue, 12 Jul 2016 09:56:33 -0400
parents 2e5a83c0f78f
children
comparison
equal deleted inserted replaced
15:48c41c6ad84e 16:55bfe9d1888e
18 "label": null, 18 "label": null,
19 "name": "Input dataset", 19 "name": "Input dataset",
20 "outputs": [], 20 "outputs": [],
21 "position": { 21 "position": {
22 "left": 200, 22 "left": 200,
23 "top": 128 23 "top": 141
24 }, 24 },
25 "tool_errors": null, 25 "tool_errors": null,
26 "tool_id": null, 26 "tool_id": null,
27 "tool_state": "{\"name\": \"Reference fasta\"}", 27 "tool_state": "{\"name\": \"Reference fasta\"}",
28 "tool_version": null, 28 "tool_version": null,
29 "type": "data_input", 29 "type": "data_input",
30 "uuid": "2f18889e-5448-460b-8167-e04125fd51cf", 30 "uuid": "108478ac-5f4a-4244-b9db-f6c0ae9674fb",
31 "workflow_outputs": [] 31 "workflow_outputs": []
32 }, 32 },
33 "1": { 33 "1": {
34 "annotation": "", 34 "annotation": "",
35 "content_id": null, 35 "content_id": null,
44 "label": null, 44 "label": null,
45 "name": "Input dataset", 45 "name": "Input dataset",
46 "outputs": [], 46 "outputs": [],
47 "position": { 47 "position": {
48 "left": 189, 48 "left": 189,
49 "top": 296 49 "top": 309
50 }, 50 },
51 "tool_errors": null, 51 "tool_errors": null,
52 "tool_id": null, 52 "tool_id": null,
53 "tool_state": "{\"name\": \"R1 fastq\"}", 53 "tool_state": "{\"name\": \"R1 fastq\"}",
54 "tool_version": null, 54 "tool_version": null,
55 "type": "data_input", 55 "type": "data_input",
56 "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c", 56 "uuid": "b00e3b0f-c7b6-4704-840b-76ec70d1cb75",
57 "workflow_outputs": [] 57 "workflow_outputs": []
58 }, 58 },
59 "2": { 59 "2": {
60 "annotation": "", 60 "annotation": "",
61 "content_id": null, 61 "content_id": null,
70 "label": null, 70 "label": null,
71 "name": "Input dataset", 71 "name": "Input dataset",
72 "outputs": [], 72 "outputs": [],
73 "position": { 73 "position": {
74 "left": 211, 74 "left": 211,
75 "top": 474 75 "top": 487
76 }, 76 },
77 "tool_errors": null, 77 "tool_errors": null,
78 "tool_id": null, 78 "tool_id": null,
79 "tool_state": "{\"name\": \"R2 fastqs\"}", 79 "tool_state": "{\"name\": \"R2 fastqs\"}",
80 "tool_version": null, 80 "tool_version": null,
81 "type": "data_input", 81 "type": "data_input",
82 "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25", 82 "uuid": "5e82d35b-0ce9-4295-a9af-0a5e35283404",
83 "workflow_outputs": [] 83 "workflow_outputs": []
84 }, 84 },
85 "3": { 85 "3": {
86 "annotation": "", 86 "annotation": "",
87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", 87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
98 "reference_source|ref_file": { 98 "reference_source|ref_file": {
99 "id": 0, 99 "id": 0,
100 "output_name": "output" 100 "output_name": "output"
101 } 101 }
102 }, 102 },
103 "inputs": [], 103 "inputs": [
104 {
105 "description": "runtime parameter for tool Map with BWA-MEM",
106 "name": "reference_source"
107 },
108 {
109 "description": "runtime parameter for tool Map with BWA-MEM",
110 "name": "fastq_input"
111 },
112 {
113 "description": "runtime parameter for tool Map with BWA-MEM",
114 "name": "fastq_input"
115 }
116 ],
104 "label": null, 117 "label": null,
105 "name": "Map with BWA-MEM", 118 "name": "Map with BWA-MEM",
106 "outputs": [ 119 "outputs": [
107 { 120 {
108 "name": "bam_output", 121 "name": "bam_output",
109 "type": "bam" 122 "type": "bam"
110 } 123 }
111 ], 124 ],
112 "position": { 125 "position": {
113 "left": 423.5, 126 "left": 423.5,
114 "top": 300 127 "top": 313
115 }, 128 },
116 "post_job_actions": { 129 "post_job_actions": {
117 "RenameDatasetActionbam_output": { 130 "RenameDatasetActionbam_output": {
118 "action_arguments": { 131 "action_arguments": {
119 "newname": "#{fastq_input1 | basename}.bam" 132 "newname": "#{fastq_input1 | basename}.bam"
122 "output_name": "bam_output" 135 "output_name": "bam_output"
123 } 136 }
124 }, 137 },
125 "tool_errors": null, 138 "tool_errors": null,
126 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", 139 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
127 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__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\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", 140 "tool_shed_repository": {
141 "changeset_revision": "546ada4a9f43",
142 "name": "bwa",
143 "owner": "devteam",
144 "tool_shed": "toolshed.g2.bx.psu.edu"
145 },
146 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"true\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"true\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"true\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
128 "tool_version": "0.7.12.1", 147 "tool_version": "0.7.12.1",
129 "type": "tool", 148 "type": "tool",
130 "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d", 149 "uuid": "f74219f9-2d53-4eca-9bb7-079a2a8aa65e",
131 "workflow_outputs": [] 150 "workflow_outputs": []
132 }, 151 },
133 "4": { 152 "4": {
134 "annotation": "", 153 "annotation": "",
135 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 154 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
142 "ref_file": { 161 "ref_file": {
143 "id": 0, 162 "id": 0,
144 "output_name": "output" 163 "output_name": "output"
145 } 164 }
146 }, 165 },
147 "inputs": [], 166 "inputs": [
167 {
168 "description": "runtime parameter for tool PHE MPileup",
169 "name": "ref_file"
170 },
171 {
172 "description": "runtime parameter for tool PHE MPileup",
173 "name": "input_bam"
174 }
175 ],
148 "label": null, 176 "label": null,
149 "name": "PHE MPileup", 177 "name": "PHE MPileup",
150 "outputs": [ 178 "outputs": [
151 { 179 {
152 "name": "outvcf", 180 "name": "outvcf",
153 "type": "vcf" 181 "type": "vcf"
154 } 182 }
155 ], 183 ],
156 "position": { 184 "position": {
157 "left": 634, 185 "left": 634,
158 "top": 138 186 "top": 151
159 }, 187 },
160 "post_job_actions": { 188 "post_job_actions": {
161 "RenameDatasetActionoutvcf": { 189 "RenameDatasetActionoutvcf": {
162 "action_arguments": { 190 "action_arguments": {
163 "newname": "#{input_bam | basename}.vcf" 191 "newname": "#{input_bam | basename}.vcf"
166 "output_name": "outvcf" 194 "output_name": "outvcf"
167 } 195 }
168 }, 196 },
169 "tool_errors": null, 197 "tool_errors": null,
170 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 198 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
171 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", 199 "tool_shed_repository": {
200 "changeset_revision": "b13db9e677b4",
201 "name": "phe_samtools_mpileup",
202 "owner": "ulfschaefer",
203 "tool_shed": "toolshed.g2.bx.psu.edu"
204 },
205 "tool_state": "{\"ref_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
172 "tool_version": "1.0", 206 "tool_version": "1.0",
173 "type": "tool", 207 "type": "tool",
174 "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca", 208 "uuid": "83294062-5c05-4a09-938a-96a409216477",
175 "workflow_outputs": [] 209 "workflow_outputs": []
176 }, 210 },
177 "5": { 211 "5": {
178 "annotation": "", 212 "annotation": "",
179 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 213 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
186 "ref_fa": { 220 "ref_fa": {
187 "id": 0, 221 "id": 0,
188 "output_name": "output" 222 "output_name": "output"
189 } 223 }
190 }, 224 },
191 "inputs": [], 225 "inputs": [
226 {
227 "description": "runtime parameter for tool Filter VCF",
228 "name": "input"
229 },
230 {
231 "description": "runtime parameter for tool Filter VCF",
232 "name": "ref_fa"
233 }
234 ],
192 "label": null, 235 "label": null,
193 "name": "Filter VCF", 236 "name": "Filter VCF",
194 "outputs": [ 237 "outputs": [
195 { 238 {
196 "name": "output", 239 "name": "output",
197 "type": "vcf" 240 "type": "vcf"
198 } 241 }
199 ], 242 ],
200 "position": { 243 "position": {
201 "left": 747, 244 "left": 747,
202 "top": 326 245 "top": 339
203 }, 246 },
204 "post_job_actions": { 247 "post_job_actions": {
205 "RenameDatasetActionoutput": { 248 "RenameDatasetActionoutput": {
206 "action_arguments": { 249 "action_arguments": {
207 "newname": "#{input | basename}.filtered.vcf" 250 "newname": "#{input | basename}.filtered.vcf"
210 "output_name": "output" 253 "output_name": "output"
211 } 254 }
212 }, 255 },
213 "tool_errors": null, 256 "tool_errors": null,
214 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 257 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
215 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}", 258 "tool_shed_repository": {
259 "changeset_revision": "48c41c6ad84e",
260 "name": "phephenix",
261 "owner": "ulfschaefer",
262 "tool_shed": "toolshed.g2.bx.psu.edu"
263 },
264 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"5\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 4, \\\"snp_filter_type\\\": {\\\"mq0f_ratio\\\": \\\"0.05\\\", \\\"__current_case__\\\": 8, \\\"snp_filter_type_selector\\\": \\\"mq0f_ratio_option\\\"}}]\"}",
216 "tool_version": "1.0", 265 "tool_version": "1.0",
217 "type": "tool", 266 "type": "tool",
218 "uuid": "51251f05-75d4-4d89-b757-2248b934d630", 267 "uuid": "9e3a724f-63e2-45c8-9d61-19643583f4bb",
219 "workflow_outputs": [] 268 "workflow_outputs": []
220 } 269 }
221 }, 270 },
222 "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf" 271 "uuid": "3392477d-d5ec-402e-b4a9-d25f79403fe9"
223 } 272 }