Mercurial > repos > stemcellcommons > chipseq_workflows
comparison TF_ChIP-Seq_analysis_using_MACS2__hg19.ga @ 5:4bf23bc4f4e2 draft
Update workflows and dependencies
author | stemcellcommons |
---|---|
date | Fri, 22 Jul 2016 00:07:10 -0400 |
parents | d60e070af736 |
children | e6d80da34425 |
comparison
equal
deleted
inserted
replaced
4:c9a9e3a09f44 | 5:4bf23bc4f4e2 |
---|---|
4 "format-version": "0.1", | 4 "format-version": "0.1", |
5 "name": "TF ChIP-Seq analysis using MACS2: hg19", | 5 "name": "TF ChIP-Seq analysis using MACS2: hg19", |
6 "steps": { | 6 "steps": { |
7 "0": { | 7 "0": { |
8 "annotation": "", | 8 "annotation": "", |
9 "content_id": null, | |
9 "id": 0, | 10 "id": 0, |
10 "input_connections": {}, | 11 "input_connections": {}, |
11 "inputs": [ | 12 "inputs": [ |
12 { | 13 { |
13 "description": "", | 14 "description": "", |
14 "name": "exp_file" | 15 "name": "exp_file" |
15 } | 16 } |
16 ], | 17 ], |
18 "label": null, | |
17 "name": "Input dataset", | 19 "name": "Input dataset", |
18 "outputs": [], | 20 "outputs": [], |
19 "position": { | 21 "position": { |
20 "left": 206, | 22 "left": 206, |
21 "top": 381.265625 | 23 "top": 381.265625 |
23 "tool_errors": null, | 25 "tool_errors": null, |
24 "tool_id": null, | 26 "tool_id": null, |
25 "tool_state": "{\"name\": \"exp_file\"}", | 27 "tool_state": "{\"name\": \"exp_file\"}", |
26 "tool_version": null, | 28 "tool_version": null, |
27 "type": "data_input", | 29 "type": "data_input", |
28 "user_outputs": [] | 30 "uuid": "f48e77b8-7d87-4b9f-bac1-6bd9748addab", |
31 "workflow_outputs": [] | |
29 }, | 32 }, |
30 "1": { | 33 "1": { |
31 "annotation": "", | 34 "annotation": "", |
35 "content_id": null, | |
32 "id": 1, | 36 "id": 1, |
33 "input_connections": {}, | 37 "input_connections": {}, |
34 "inputs": [ | 38 "inputs": [ |
35 { | 39 { |
36 "description": "", | 40 "description": "", |
37 "name": "input_file" | 41 "name": "input_file" |
38 } | 42 } |
39 ], | 43 ], |
44 "label": null, | |
40 "name": "Input dataset", | 45 "name": "Input dataset", |
41 "outputs": [], | 46 "outputs": [], |
42 "position": { | 47 "position": { |
43 "left": 201, | 48 "left": 201, |
44 "top": 516.265625 | 49 "top": 516.265625 |
46 "tool_errors": null, | 51 "tool_errors": null, |
47 "tool_id": null, | 52 "tool_id": null, |
48 "tool_state": "{\"name\": \"input_file\"}", | 53 "tool_state": "{\"name\": \"input_file\"}", |
49 "tool_version": null, | 54 "tool_version": null, |
50 "type": "data_input", | 55 "type": "data_input", |
51 "user_outputs": [] | 56 "uuid": "d38090b9-b25b-4fea-948e-f5818b1d2d4f", |
57 "workflow_outputs": [] | |
52 }, | 58 }, |
53 "2": { | 59 "2": { |
54 "annotation": "", | 60 "annotation": "", |
61 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", | |
55 "id": 2, | 62 "id": 2, |
56 "input_connections": { | 63 "input_connections": { |
57 "input_file": { | 64 "input_file": { |
58 "id": 0, | 65 "id": 0, |
59 "output_name": "output" | 66 "output_name": "output" |
60 } | 67 } |
61 }, | 68 }, |
62 "inputs": [], | 69 "inputs": [ |
70 { | |
71 "description": "runtime parameter for tool FASTQ Parallel Groomer", | |
72 "name": "input_file" | |
73 } | |
74 ], | |
75 "label": null, | |
63 "name": "FASTQ Parallel Groomer", | 76 "name": "FASTQ Parallel Groomer", |
64 "outputs": [ | 77 "outputs": [ |
65 { | 78 { |
66 "name": "output_file", | 79 "name": "output_file", |
67 "type": "fastqsanger" | 80 "type": "fastqsanger" |
72 "top": 341.265625 | 85 "top": 341.265625 |
73 }, | 86 }, |
74 "post_job_actions": {}, | 87 "post_job_actions": {}, |
75 "tool_errors": null, | 88 "tool_errors": null, |
76 "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", |
77 "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\\\"}\"}", | |
78 "tool_version": "0.3.1", | 97 "tool_version": "0.3.1", |
79 "type": "tool", | 98 "type": "tool", |
80 "user_outputs": [] | 99 "uuid": "c2e08189-33e3-40bf-a914-cfdb726734e5", |
100 "workflow_outputs": [] | |
81 }, | 101 }, |
82 "3": { | 102 "3": { |
83 "annotation": "", | 103 "annotation": "", |
104 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", | |
84 "id": 3, | 105 "id": 3, |
85 "input_connections": { | 106 "input_connections": { |
86 "input_file": { | 107 "input_file": { |
87 "id": 1, | 108 "id": 1, |
88 "output_name": "output" | 109 "output_name": "output" |
89 } | 110 } |
90 }, | 111 }, |
91 "inputs": [], | 112 "inputs": [ |
113 { | |
114 "description": "runtime parameter for tool FASTQ Parallel Groomer", | |
115 "name": "input_file" | |
116 } | |
117 ], | |
118 "label": null, | |
92 "name": "FASTQ Parallel Groomer", | 119 "name": "FASTQ Parallel Groomer", |
93 "outputs": [ | 120 "outputs": [ |
94 { | 121 { |
95 "name": "output_file", | 122 "name": "output_file", |
96 "type": "fastqsanger" | 123 "type": "fastqsanger" |
101 "top": 493.265625 | 128 "top": 493.265625 |
102 }, | 129 }, |
103 "post_job_actions": {}, | 130 "post_job_actions": {}, |
104 "tool_errors": null, | 131 "tool_errors": null, |
105 "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", |
106 "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\\\"}\"}", | |
107 "tool_version": "0.3.1", | 140 "tool_version": "0.3.1", |
108 "type": "tool", | 141 "type": "tool", |
109 "user_outputs": [] | 142 "uuid": "7b72130c-3620-4406-b127-aa2d7a1323db", |
143 "workflow_outputs": [] | |
110 }, | 144 }, |
111 "4": { | 145 "4": { |
112 "annotation": "", | 146 "annotation": "", |
147 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", | |
113 "id": 4, | 148 "id": 4, |
114 "input_connections": { | 149 "input_connections": { |
115 "singlePaired|sInput1": { | 150 "singlePaired|sInput1": { |
116 "id": 2, | 151 "id": 2, |
117 "output_name": "output_file" | 152 "output_name": "output_file" |
118 } | 153 } |
119 }, | 154 }, |
120 "inputs": [], | 155 "inputs": [ |
156 { | |
157 "description": "runtime parameter for tool Map with Bowtie for Illumina", | |
158 "name": "singlePaired" | |
159 } | |
160 ], | |
161 "label": null, | |
121 "name": "Map with Bowtie for Illumina", | 162 "name": "Map with Bowtie for Illumina", |
122 "outputs": [ | 163 "outputs": [ |
123 { | 164 { |
124 "name": "output", | 165 "name": "output", |
125 "type": "sam" | 166 "type": "sam" |
146 "top": 272.265625 | 187 "top": 272.265625 |
147 }, | 188 }, |
148 "post_job_actions": {}, | 189 "post_job_actions": {}, |
149 "tool_errors": null, | 190 "tool_errors": null, |
150 "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", |
151 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__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\\\": \\\"hg19\\\", \\\"__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}\"}", | |
152 "tool_version": "1.1.3", | 199 "tool_version": "1.1.3", |
153 "type": "tool", | 200 "type": "tool", |
154 "user_outputs": [] | 201 "uuid": "c90992f7-766c-4395-b9c4-da4bd2e51840", |
202 "workflow_outputs": [] | |
155 }, | 203 }, |
156 "5": { | 204 "5": { |
157 "annotation": "", | 205 "annotation": "", |
206 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", | |
158 "id": 5, | 207 "id": 5, |
159 "input_connections": { | 208 "input_connections": { |
160 "singlePaired|sInput1": { | 209 "singlePaired|sInput1": { |
161 "id": 3, | 210 "id": 3, |
162 "output_name": "output_file" | 211 "output_name": "output_file" |
163 } | 212 } |
164 }, | 213 }, |
165 "inputs": [], | 214 "inputs": [ |
215 { | |
216 "description": "runtime parameter for tool Map with Bowtie for Illumina", | |
217 "name": "singlePaired" | |
218 } | |
219 ], | |
220 "label": null, | |
166 "name": "Map with Bowtie for Illumina", | 221 "name": "Map with Bowtie for Illumina", |
167 "outputs": [ | 222 "outputs": [ |
168 { | 223 { |
169 "name": "output", | 224 "name": "output", |
170 "type": "sam" | 225 "type": "sam" |
191 "top": 492.265625 | 246 "top": 492.265625 |
192 }, | 247 }, |
193 "post_job_actions": {}, | 248 "post_job_actions": {}, |
194 "tool_errors": null, | 249 "tool_errors": null, |
195 "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", |
196 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__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\\\": \\\"hg19\\\", \\\"__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}\"}", | |
197 "tool_version": "1.1.3", | 258 "tool_version": "1.1.3", |
198 "type": "tool", | 259 "type": "tool", |
199 "user_outputs": [] | 260 "uuid": "3d32d656-7912-44e6-a632-218286b7f916", |
261 "workflow_outputs": [] | |
200 }, | 262 }, |
201 "6": { | 263 "6": { |
202 "annotation": "", | 264 "annotation": "", |
265 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", | |
203 "id": 6, | 266 "id": 6, |
204 "input_connections": { | 267 "input_connections": { |
205 "source|input1": { | 268 "source|input1": { |
206 "id": 4, | 269 "id": 4, |
207 "output_name": "output" | 270 "output_name": "output" |
208 } | 271 } |
209 }, | 272 }, |
210 "inputs": [], | 273 "inputs": [ |
274 { | |
275 "description": "runtime parameter for tool SAM-to-BAM", | |
276 "name": "source" | |
277 } | |
278 ], | |
279 "label": null, | |
211 "name": "SAM-to-BAM", | 280 "name": "SAM-to-BAM", |
212 "outputs": [ | 281 "outputs": [ |
213 { | 282 { |
214 "name": "output1", | 283 "name": "output1", |
215 "type": "bam" | 284 "type": "bam" |
219 "left": 1069.5, | 288 "left": 1069.5, |
220 "top": 376.265625 | 289 "top": 376.265625 |
221 }, | 290 }, |
222 "post_job_actions": {}, | 291 "post_job_actions": {}, |
223 "tool_errors": null, | 292 "tool_errors": null, |
224 "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", |
225 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19full\\\"}, \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | 294 "tool_shed_repository": { |
226 "tool_version": "2.1", | 295 "changeset_revision": "d04d9f1c6791", |
227 "type": "tool", | 296 "name": "sam_to_bam", |
228 "user_outputs": [] | 297 "owner": "devteam", |
298 "tool_shed": "toolshed.g2.bx.psu.edu" | |
299 }, | |
300 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"hg19\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
301 "tool_version": "2.0", | |
302 "type": "tool", | |
303 "uuid": "7181b07a-7d15-4716-ae59-9a1084d445f3", | |
304 "workflow_outputs": [] | |
229 }, | 305 }, |
230 "7": { | 306 "7": { |
231 "annotation": "", | 307 "annotation": "", |
308 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", | |
232 "id": 7, | 309 "id": 7, |
233 "input_connections": { | 310 "input_connections": { |
234 "source|input1": { | 311 "source|input1": { |
235 "id": 5, | 312 "id": 5, |
236 "output_name": "output" | 313 "output_name": "output" |
237 } | 314 } |
238 }, | 315 }, |
239 "inputs": [], | 316 "inputs": [ |
317 { | |
318 "description": "runtime parameter for tool SAM-to-BAM", | |
319 "name": "source" | |
320 } | |
321 ], | |
322 "label": null, | |
240 "name": "SAM-to-BAM", | 323 "name": "SAM-to-BAM", |
241 "outputs": [ | 324 "outputs": [ |
242 { | 325 { |
243 "name": "output1", | 326 "name": "output1", |
244 "type": "bam" | 327 "type": "bam" |
248 "left": 1071.5, | 331 "left": 1071.5, |
249 "top": 533.265625 | 332 "top": 533.265625 |
250 }, | 333 }, |
251 "post_job_actions": {}, | 334 "post_job_actions": {}, |
252 "tool_errors": null, | 335 "tool_errors": null, |
253 "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", |
254 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19full\\\"}, \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | 337 "tool_shed_repository": { |
255 "tool_version": "2.1", | 338 "changeset_revision": "d04d9f1c6791", |
256 "type": "tool", | 339 "name": "sam_to_bam", |
257 "user_outputs": [] | 340 "owner": "devteam", |
341 "tool_shed": "toolshed.g2.bx.psu.edu" | |
342 }, | |
343 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"hg19\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
344 "tool_version": "2.0", | |
345 "type": "tool", | |
346 "uuid": "37977857-377d-4e5f-b256-fae093d920de", | |
347 "workflow_outputs": [] | |
258 }, | 348 }, |
259 "8": { | 349 "8": { |
260 "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\"}}", |
351 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", | |
261 "id": 8, | 352 "id": 8, |
262 "input_connections": { | 353 "input_connections": { |
263 "input_control_file": { | 354 "input_control_file": { |
264 "id": 7, | 355 "id": 7, |
265 "output_name": "output1" | 356 "output_name": "output1" |
267 "input_treatment_file": { | 358 "input_treatment_file": { |
268 "id": 6, | 359 "id": 6, |
269 "output_name": "output1" | 360 "output_name": "output1" |
270 } | 361 } |
271 }, | 362 }, |
272 "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 ], | |
373 "label": null, | |
273 "name": "MACS2 callpeak", | 374 "name": "MACS2 callpeak", |
274 "outputs": [ | 375 "outputs": [ |
275 { | 376 { |
276 "name": "output_tabular", | 377 "name": "output_tabular", |
277 "type": "tabular" | 378 "type": "tabular" |
314 "top": 358.5 | 415 "top": 358.5 |
315 }, | 416 }, |
316 "post_job_actions": {}, | 417 "post_job_actions": {}, |
317 "tool_errors": null, | 418 "tool_errors": null, |
318 "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", |
319 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2451960000\\\", \\\"__current_case__\\\": 0}\", \"bampe\": \"\\\"False\\\"\", \"input_control_file\": \"null\", \"__rerun_remap_job_id__\": null, \"band_width\": \"\\\"300\\\"\", \"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}\", \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\"}", | 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\\\": \\\"2451960000\\\", \\\"__current_case__\\\": 0}\", \"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\\\"\"}", | |
320 "tool_version": "2.1.0.20151222.0", | 427 "tool_version": "2.1.0.20151222.0", |
321 "type": "tool", | 428 "type": "tool", |
322 "user_outputs": [] | 429 "uuid": "7d522e1b-10c7-41d6-8fee-455133c85089", |
430 "workflow_outputs": [] | |
323 }, | 431 }, |
324 "9": { | 432 "9": { |
325 "annotation": "", | 433 "annotation": "", |
434 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", | |
326 "id": 9, | 435 "id": 9, |
327 "input_connections": { | 436 "input_connections": { |
328 "infile_control": { | 437 "infile_control": { |
329 "id": 8, | 438 "id": 8, |
330 "output_name": "output_control_lambda" | 439 "output_name": "output_control_lambda" |
332 "infile_treatment": { | 441 "infile_treatment": { |
333 "id": 8, | 442 "id": 8, |
334 "output_name": "output_treat_pileup" | 443 "output_name": "output_treat_pileup" |
335 } | 444 } |
336 }, | 445 }, |
337 "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 ], | |
456 "label": null, | |
338 "name": "MACS2 bdgcmp", | 457 "name": "MACS2 bdgcmp", |
339 "outputs": [ | 458 "outputs": [ |
340 { | 459 { |
341 "name": "outfile", | 460 "name": "outfile", |
342 "type": "bedgraph" | 461 "type": "bedgraph" |
347 "top": 426.5 | 466 "top": 426.5 |
348 }, | 467 }, |
349 "post_job_actions": {}, | 468 "post_job_actions": {}, |
350 "tool_errors": null, | 469 "tool_errors": null, |
351 "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", |
352 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"infile_treatment\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\"}", | 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\\\"}\"}", | |
353 "tool_version": "2.1.0.20151222.0", | 478 "tool_version": "2.1.0.20151222.0", |
354 "type": "tool", | 479 "type": "tool", |
355 "user_outputs": [] | 480 "uuid": "dcfd9cac-e8a2-4425-a8fc-1e398710d6ca", |
481 "workflow_outputs": [] | |
356 }, | 482 }, |
357 "10": { | 483 "10": { |
358 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", | 484 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", |
485 "content_id": "wig_to_bigWig", | |
359 "id": 10, | 486 "id": 10, |
360 "input_connections": { | 487 "input_connections": { |
361 "input1": { | 488 "input1": { |
362 "id": 9, | 489 "id": 9, |
363 "output_name": "outfile" | 490 "output_name": "outfile" |
364 } | 491 } |
365 }, | 492 }, |
366 "inputs": [], | 493 "inputs": [ |
494 { | |
495 "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", | |
496 "name": "input1" | |
497 } | |
498 ], | |
499 "label": null, | |
367 "name": "Wig/BedGraph-to-bigWig", | 500 "name": "Wig/BedGraph-to-bigWig", |
368 "outputs": [ | 501 "outputs": [ |
369 { | 502 { |
370 "name": "out_file1", | 503 "name": "out_file1", |
371 "type": "bigwig" | 504 "type": "bigwig" |
376 "top": 447.71875 | 509 "top": 447.71875 |
377 }, | 510 }, |
378 "post_job_actions": {}, | 511 "post_job_actions": {}, |
379 "tool_errors": null, | 512 "tool_errors": null, |
380 "tool_id": "wig_to_bigWig", | 513 "tool_id": "wig_to_bigWig", |
381 "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}\"}", |
382 "tool_version": "1.1.0", | 515 "tool_version": "1.1.0", |
383 "type": "tool", | 516 "type": "tool", |
384 "user_outputs": [] | 517 "uuid": "f5cf8c55-03d2-4fc0-b5fa-5f4be859b628", |
518 "workflow_outputs": [] | |
385 } | 519 } |
386 } | 520 }, |
521 "uuid": "9d3dbd7d-2fd7-479f-a582-aa2d84a5d443" | |
387 } | 522 } |