Mercurial > repos > stemcellcommons > chipseq_workflows

comparison TF_ChIP-Seq_analysis_using_MACS2__mm10.ga @ 5:4bf23bc4f4e2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update workflows and dependencies
author stemcellcommons
date Fri, 22 Jul 2016 00:07:10 -0400
parents cfae7747e902
children f9ffbe563402
comparison
equal deleted inserted replaced
4:c9a9e3a09f44 5:4bf23bc4f4e2
25 "tool_errors": null, 25 "tool_errors": null,
26 "tool_id": null, 26 "tool_id": null,
27 "tool_state": "{\"name\": \"exp_file\"}", 27 "tool_state": "{\"name\": \"exp_file\"}",
28 "tool_version": null, 28 "tool_version": null,
29 "type": "data_input", 29 "type": "data_input",
30 "uuid": "dd984d64-daac-4547-9989-9303056523d3", 30 "uuid": "77699462-04dc-4480-a351-c3ba909c94d9",
31 "workflow_outputs": [] 31 "workflow_outputs": []
32 }, 32 },
33 "1": { 33 "1": {
34 "annotation": "", 34 "annotation": "",
35 "content_id": null, 35 "content_id": null,
51 "tool_errors": null, 51 "tool_errors": null,
52 "tool_id": null, 52 "tool_id": null,
53 "tool_state": "{\"name\": \"input_file\"}", 53 "tool_state": "{\"name\": \"input_file\"}",
54 "tool_version": null, 54 "tool_version": null,
55 "type": "data_input", 55 "type": "data_input",
56 "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", 56 "uuid": "87084ec7-ede5-4f5a-a49c-5f96c169daa7",
57 "workflow_outputs": [] 57 "workflow_outputs": []
58 }, 58 },
59 "2": { 59 "2": {
60 "annotation": "", 60 "annotation": "",
61 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 61 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
64 "input_file": { 64 "input_file": {
65 "id": 0, 65 "id": 0,
66 "output_name": "output" 66 "output_name": "output"
67 } 67 }
68 }, 68 },
69 "inputs": [], 69 "inputs": [
70 {
71 "description": "runtime parameter for tool FASTQ Parallel Groomer",
72 "name": "input_file"
73 }
74 ],
70 "label": null, 75 "label": null,
71 "name": "FASTQ Parallel Groomer", 76 "name": "FASTQ Parallel Groomer",
72 "outputs": [ 77 "outputs": [
73 { 78 {
74 "name": "output_file", 79 "name": "output_file",
80 "top": 341.265625 85 "top": 341.265625
81 }, 86 },
82 "post_job_actions": {}, 87 "post_job_actions": {},
83 "tool_errors": null, 88 "tool_errors": null,
84 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 89 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
85 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", 90 "tool_shed_repository": {
91 "changeset_revision": "66ca0d174cf2",
92 "name": "fastq_groomer_parallel",
93 "owner": "kevyin",
94 "tool_shed": "toolshed.g2.bx.psu.edu"
95 },
96 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
86 "tool_version": "0.3.1", 97 "tool_version": "0.3.1",
87 "type": "tool", 98 "type": "tool",
88 "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", 99 "uuid": "a91fcfa1-2ad2-4d1b-af4e-8c348ca99cf4",
89 "workflow_outputs": [] 100 "workflow_outputs": []
90 }, 101 },
91 "3": { 102 "3": {
92 "annotation": "", 103 "annotation": "",
93 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 104 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
96 "input_file": { 107 "input_file": {
97 "id": 1, 108 "id": 1,
98 "output_name": "output" 109 "output_name": "output"
99 } 110 }
100 }, 111 },
101 "inputs": [], 112 "inputs": [
113 {
114 "description": "runtime parameter for tool FASTQ Parallel Groomer",
115 "name": "input_file"
116 }
117 ],
102 "label": null, 118 "label": null,
103 "name": "FASTQ Parallel Groomer", 119 "name": "FASTQ Parallel Groomer",
104 "outputs": [ 120 "outputs": [
105 { 121 {
106 "name": "output_file", 122 "name": "output_file",
112 "top": 493.265625 128 "top": 493.265625
113 }, 129 },
114 "post_job_actions": {}, 130 "post_job_actions": {},
115 "tool_errors": null, 131 "tool_errors": null,
116 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 132 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
117 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", 133 "tool_shed_repository": {
134 "changeset_revision": "66ca0d174cf2",
135 "name": "fastq_groomer_parallel",
136 "owner": "kevyin",
137 "tool_shed": "toolshed.g2.bx.psu.edu"
138 },
139 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
118 "tool_version": "0.3.1", 140 "tool_version": "0.3.1",
119 "type": "tool", 141 "type": "tool",
120 "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", 142 "uuid": "93829f40-3abf-4aa3-8951-46b67cf86a95",
121 "workflow_outputs": [] 143 "workflow_outputs": []
122 }, 144 },
123 "4": { 145 "4": {
124 "annotation": "", 146 "annotation": "",
125 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 147 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
128 "singlePaired|sInput1": { 150 "singlePaired|sInput1": {
129 "id": 2, 151 "id": 2,
130 "output_name": "output_file" 152 "output_name": "output_file"
131 } 153 }
132 }, 154 },
133 "inputs": [], 155 "inputs": [
156 {
157 "description": "runtime parameter for tool Map with Bowtie for Illumina",
158 "name": "singlePaired"
159 }
160 ],
134 "label": null, 161 "label": null,
135 "name": "Map with Bowtie for Illumina", 162 "name": "Map with Bowtie for Illumina",
136 "outputs": [ 163 "outputs": [
137 { 164 {
138 "name": "output", 165 "name": "output",
160 "top": 272.265625 187 "top": 272.265625
161 }, 188 },
162 "post_job_actions": {}, 189 "post_job_actions": {},
163 "tool_errors": null, 190 "tool_errors": null,
164 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 191 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
165 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 192 "tool_shed_repository": {
193 "changeset_revision": "df86f29bedee",
194 "name": "bowtie_wrappers",
195 "owner": "devteam",
196 "tool_shed": "toolshed.g2.bx.psu.edu"
197 },
198 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
166 "tool_version": "1.1.3", 199 "tool_version": "1.1.3",
167 "type": "tool", 200 "type": "tool",
168 "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", 201 "uuid": "9ec994d9-7309-4655-b3d8-cca2de8de69b",
169 "workflow_outputs": [] 202 "workflow_outputs": []
170 }, 203 },
171 "5": { 204 "5": {
172 "annotation": "", 205 "annotation": "",
173 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 206 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
176 "singlePaired|sInput1": { 209 "singlePaired|sInput1": {
177 "id": 3, 210 "id": 3,
178 "output_name": "output_file" 211 "output_name": "output_file"
179 } 212 }
180 }, 213 },
181 "inputs": [], 214 "inputs": [
215 {
216 "description": "runtime parameter for tool Map with Bowtie for Illumina",
217 "name": "singlePaired"
218 }
219 ],
182 "label": null, 220 "label": null,
183 "name": "Map with Bowtie for Illumina", 221 "name": "Map with Bowtie for Illumina",
184 "outputs": [ 222 "outputs": [
185 { 223 {
186 "name": "output", 224 "name": "output",
208 "top": 492.265625 246 "top": 492.265625
209 }, 247 },
210 "post_job_actions": {}, 248 "post_job_actions": {},
211 "tool_errors": null, 249 "tool_errors": null,
212 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 250 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
213 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 251 "tool_shed_repository": {
252 "changeset_revision": "df86f29bedee",
253 "name": "bowtie_wrappers",
254 "owner": "devteam",
255 "tool_shed": "toolshed.g2.bx.psu.edu"
256 },
257 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
214 "tool_version": "1.1.3", 258 "tool_version": "1.1.3",
215 "type": "tool", 259 "type": "tool",
216 "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677", 260 "uuid": "20e8c743-50c8-4afa-9fda-54b0207d7e8f",
217 "workflow_outputs": [] 261 "workflow_outputs": []
218 }, 262 },
219 "6": { 263 "6": {
220 "annotation": "", 264 "annotation": "",
221 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 265 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
222 "id": 6, 266 "id": 6,
223 "input_connections": { 267 "input_connections": {
224 "source|input1": { 268 "source|input1": {
225 "id": 4, 269 "id": 4,
226 "output_name": "output" 270 "output_name": "output"
227 } 271 }
228 }, 272 },
229 "inputs": [], 273 "inputs": [
274 {
275 "description": "runtime parameter for tool SAM-to-BAM",
276 "name": "source"
277 }
278 ],
230 "label": null, 279 "label": null,
231 "name": "SAM-to-BAM", 280 "name": "SAM-to-BAM",
232 "outputs": [ 281 "outputs": [
233 { 282 {
234 "name": "output1", 283 "name": "output1",
239 "left": 1070.5, 288 "left": 1070.5,
240 "top": 376.265625 289 "top": 376.265625
241 }, 290 },
242 "post_job_actions": {}, 291 "post_job_actions": {},
243 "tool_errors": null, 292 "tool_errors": null,
244 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 293 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
245 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 294 "tool_shed_repository": {
246 "tool_version": "2.1", 295 "changeset_revision": "d04d9f1c6791",
247 "type": "tool", 296 "name": "sam_to_bam",
248 "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", 297 "owner": "devteam",
298 "tool_shed": "toolshed.g2.bx.psu.edu"
299 },
300 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
301 "tool_version": "2.0",
302 "type": "tool",
303 "uuid": "5c875347-40cd-4522-a57a-ca380f976df4",
249 "workflow_outputs": [] 304 "workflow_outputs": []
250 }, 305 },
251 "7": { 306 "7": {
252 "annotation": "", 307 "annotation": "",
253 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 308 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
254 "id": 7, 309 "id": 7,
255 "input_connections": { 310 "input_connections": {
256 "source|input1": { 311 "source|input1": {
257 "id": 5, 312 "id": 5,
258 "output_name": "output" 313 "output_name": "output"
259 } 314 }
260 }, 315 },
261 "inputs": [], 316 "inputs": [
317 {
318 "description": "runtime parameter for tool SAM-to-BAM",
319 "name": "source"
320 }
321 ],
262 "label": null, 322 "label": null,
263 "name": "SAM-to-BAM", 323 "name": "SAM-to-BAM",
264 "outputs": [ 324 "outputs": [
265 { 325 {
266 "name": "output1", 326 "name": "output1",
271 "left": 1071.5, 331 "left": 1071.5,
272 "top": 533.265625 332 "top": 533.265625
273 }, 333 },
274 "post_job_actions": {}, 334 "post_job_actions": {},
275 "tool_errors": null, 335 "tool_errors": null,
276 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 336 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
277 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 337 "tool_shed_repository": {
278 "tool_version": "2.1", 338 "changeset_revision": "d04d9f1c6791",
279 "type": "tool", 339 "name": "sam_to_bam",
280 "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", 340 "owner": "devteam",
341 "tool_shed": "toolshed.g2.bx.psu.edu"
342 },
343 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
344 "tool_version": "2.0",
345 "type": "tool",
346 "uuid": "6f3e360c-d5b4-46bb-9a3d-e56c78651cee",
281 "workflow_outputs": [] 347 "workflow_outputs": []
282 }, 348 },
283 "8": { 349 "8": {
284 "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}", 350 "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}",
285 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", 351 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
292 "input_treatment_file": { 358 "input_treatment_file": {
293 "id": 6, 359 "id": 6,
294 "output_name": "output1" 360 "output_name": "output1"
295 } 361 }
296 }, 362 },
297 "inputs": [], 363 "inputs": [
364 {
365 "description": "runtime parameter for tool MACS2 callpeak",
366 "name": "input_control_file"
367 },
368 {
369 "description": "runtime parameter for tool MACS2 callpeak",
370 "name": "input_treatment_file"
371 }
372 ],
298 "label": null, 373 "label": null,
299 "name": "MACS2 callpeak", 374 "name": "MACS2 callpeak",
300 "outputs": [ 375 "outputs": [
301 { 376 {
302 "name": "output_tabular", 377 "name": "output_tabular",
340 "top": 358.5 415 "top": 358.5
341 }, 416 },
342 "post_job_actions": {}, 417 "post_job_actions": {},
343 "tool_errors": null, 418 "tool_errors": null,
344 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", 419 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
345 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"False\\\"\", \"input_control_file\": \"null\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"null\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", 420 "tool_shed_repository": {
421 "changeset_revision": "6d4babad010f",
422 "name": "macs2",
423 "owner": "iuc",
424 "tool_shed": "toolshed.g2.bx.psu.edu"
425 },
426 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}",
346 "tool_version": "2.1.0.20151222.0", 427 "tool_version": "2.1.0.20151222.0",
347 "type": "tool", 428 "type": "tool",
348 "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", 429 "uuid": "bbcb3034-f9af-4b45-b877-54822312ddac",
349 "workflow_outputs": [] 430 "workflow_outputs": []
350 }, 431 },
351 "9": { 432 "9": {
352 "annotation": "", 433 "annotation": "",
353 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", 434 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
360 "infile_treatment": { 441 "infile_treatment": {
361 "id": 8, 442 "id": 8,
362 "output_name": "output_treat_pileup" 443 "output_name": "output_treat_pileup"
363 } 444 }
364 }, 445 },
365 "inputs": [], 446 "inputs": [
447 {
448 "description": "runtime parameter for tool MACS2 bdgcmp",
449 "name": "infile_control"
450 },
451 {
452 "description": "runtime parameter for tool MACS2 bdgcmp",
453 "name": "infile_treatment"
454 }
455 ],
366 "label": null, 456 "label": null,
367 "name": "MACS2 bdgcmp", 457 "name": "MACS2 bdgcmp",
368 "outputs": [ 458 "outputs": [
369 { 459 {
370 "name": "outfile", 460 "name": "outfile",
376 "top": 426.5 466 "top": 426.5
377 }, 467 },
378 "post_job_actions": {}, 468 "post_job_actions": {},
379 "tool_errors": null, 469 "tool_errors": null,
380 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", 470 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
381 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", 471 "tool_shed_repository": {
472 "changeset_revision": "6d4babad010f",
473 "name": "macs2",
474 "owner": "iuc",
475 "tool_shed": "toolshed.g2.bx.psu.edu"
476 },
477 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
382 "tool_version": "2.1.0.20151222.0", 478 "tool_version": "2.1.0.20151222.0",
383 "type": "tool", 479 "type": "tool",
384 "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", 480 "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41",
385 "workflow_outputs": [] 481 "workflow_outputs": []
386 }, 482 },
387 "10": { 483 "10": {
388 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", 484 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}",
389 "content_id": "wig_to_bigWig", 485 "content_id": "wig_to_bigWig",
392 "input1": { 488 "input1": {
393 "id": 9, 489 "id": 9,
394 "output_name": "outfile" 490 "output_name": "outfile"
395 } 491 }
396 }, 492 },
397 "inputs": [], 493 "inputs": [
494 {
495 "description": "runtime parameter for tool Wig/BedGraph-to-bigWig",
496 "name": "input1"
497 }
498 ],
398 "label": null, 499 "label": null,
399 "name": "Wig/BedGraph-to-bigWig", 500 "name": "Wig/BedGraph-to-bigWig",
400 "outputs": [ 501 "outputs": [
401 { 502 {
402 "name": "out_file1", 503 "name": "out_file1",
408 "top": 447.71875 509 "top": 447.71875
409 }, 510 },
410 "post_job_actions": {}, 511 "post_job_actions": {},
411 "tool_errors": null, 512 "tool_errors": null,
412 "tool_id": "wig_to_bigWig", 513 "tool_id": "wig_to_bigWig",
413 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 514 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}",
414 "tool_version": "1.1.0", 515 "tool_version": "1.1.0",
415 "type": "tool", 516 "type": "tool",
416 "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", 517 "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a",
417 "workflow_outputs": [] 518 "workflow_outputs": []
418 } 519 }
419 }, 520 },
420 "uuid": "a2493925-4c14-413d-89d6-0b3ba2395dbe" 521 "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4"
421 } 522 }