Mercurial > repos > stemcellcommons > rnaseq_workflows
comparison RNA-seq_paired_end_with_TopHat_-_hg19.ga @ 0:cbd6667ca478 draft
Initial upload
author | stemcellcommons |
---|---|
date | Wed, 20 Jul 2016 16:58:05 -0400 |
parents | |
children | ba1b76257fa5 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:cbd6667ca478 |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"forward_reads\", \"set2\": \"reverse_reads\"}]}", | |
4 "format-version": "0.1", | |
5 "name": "RNA-seq paired end with TopHat - hg19", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "content_id": null, | |
10 "id": 0, | |
11 "input_connections": {}, | |
12 "inputs": [ | |
13 { | |
14 "description": "", | |
15 "name": "forward_reads" | |
16 } | |
17 ], | |
18 "label": null, | |
19 "name": "Input dataset", | |
20 "outputs": [], | |
21 "position": { | |
22 "left": 207, | |
23 "top": 300 | |
24 }, | |
25 "tool_errors": null, | |
26 "tool_id": null, | |
27 "tool_state": "{\"name\": \"forward_reads\"}", | |
28 "tool_version": null, | |
29 "type": "data_input", | |
30 "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", | |
31 "workflow_outputs": [] | |
32 }, | |
33 "1": { | |
34 "annotation": "", | |
35 "content_id": null, | |
36 "id": 1, | |
37 "input_connections": {}, | |
38 "inputs": [ | |
39 { | |
40 "description": "", | |
41 "name": "reverse_reads" | |
42 } | |
43 ], | |
44 "label": null, | |
45 "name": "Input dataset", | |
46 "outputs": [], | |
47 "position": { | |
48 "left": 205, | |
49 "top": 437 | |
50 }, | |
51 "tool_errors": null, | |
52 "tool_id": null, | |
53 "tool_state": "{\"name\": \"reverse_reads\"}", | |
54 "tool_version": null, | |
55 "type": "data_input", | |
56 "uuid": "d2dbe3db-13ca-4155-a60a-cf408e53cb3a", | |
57 "workflow_outputs": [] | |
58 }, | |
59 "2": { | |
60 "annotation": "", | |
61 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", | |
62 "id": 2, | |
63 "input_connections": { | |
64 "input_file": { | |
65 "id": 0, | |
66 "output_name": "output" | |
67 } | |
68 }, | |
69 "inputs": [], | |
70 "label": null, | |
71 "name": "FASTQ Parallel Groomer", | |
72 "outputs": [ | |
73 { | |
74 "name": "output_file", | |
75 "type": "fastqsanger" | |
76 } | |
77 ], | |
78 "position": { | |
79 "left": 455.5, | |
80 "top": 259 | |
81 }, | |
82 "post_job_actions": {}, | |
83 "tool_errors": null, | |
84 "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\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", | |
86 "tool_version": "0.3.1", | |
87 "type": "tool", | |
88 "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", | |
89 "workflow_outputs": [] | |
90 }, | |
91 "3": { | |
92 "annotation": "", | |
93 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", | |
94 "id": 3, | |
95 "input_connections": { | |
96 "input_file": { | |
97 "id": 1, | |
98 "output_name": "output" | |
99 } | |
100 }, | |
101 "inputs": [], | |
102 "label": null, | |
103 "name": "FASTQ Parallel Groomer", | |
104 "outputs": [ | |
105 { | |
106 "name": "output_file", | |
107 "type": "fastqsanger" | |
108 } | |
109 ], | |
110 "position": { | |
111 "left": 456.5, | |
112 "top": 475 | |
113 }, | |
114 "post_job_actions": {}, | |
115 "tool_errors": null, | |
116 "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\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", | |
118 "tool_version": "0.3.1", | |
119 "type": "tool", | |
120 "uuid": "7b504a0d-37d1-4a2c-9cba-0cc138331375", | |
121 "workflow_outputs": [] | |
122 }, | |
123 "4": { | |
124 "annotation": "", | |
125 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | |
126 "id": 4, | |
127 "input_connections": { | |
128 "paired_end|paired_input_type_conditional|fastq_r1_in": { | |
129 "id": 2, | |
130 "output_name": "output_file" | |
131 }, | |
132 "paired_end|paired_input_type_conditional|fastq_r2_in": { | |
133 "id": 3, | |
134 "output_name": "output_file" | |
135 } | |
136 }, | |
137 "inputs": [], | |
138 "label": null, | |
139 "name": "Trimmomatic", | |
140 "outputs": [ | |
141 { | |
142 "name": "fastq_out_paired", | |
143 "type": "input" | |
144 }, | |
145 { | |
146 "name": "fastq_out_unpaired", | |
147 "type": "input" | |
148 }, | |
149 { | |
150 "name": "fastq_out_r1_paired", | |
151 "type": "fastqsanger" | |
152 }, | |
153 { | |
154 "name": "fastq_out_r2_paired", | |
155 "type": "fastqsanger" | |
156 }, | |
157 { | |
158 "name": "fastq_out_r1_unpaired", | |
159 "type": "fastqsanger" | |
160 }, | |
161 { | |
162 "name": "fastq_out_r2_unpaired", | |
163 "type": "fastqsanger" | |
164 }, | |
165 { | |
166 "name": "fastq_out", | |
167 "type": "fastqsanger" | |
168 } | |
169 ], | |
170 "position": { | |
171 "left": 791, | |
172 "top": 282 | |
173 }, | |
174 "post_job_actions": {}, | |
175 "tool_errors": null, | |
176 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | |
177 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"seed_mismatches\\\": \\\"2\\\", \\\"adapter_fasta\\\": \\\"TruSeq3-SE.fa\\\", \\\"__current_case__\\\": 0, \\\"palindrome_clip_threshold\\\": \\\"30\\\", \\\"do_illuminaclip\\\": \\\"True\\\", \\\"simple_clip_threshold\\\": \\\"10\\\"}\"}", | |
178 "tool_version": "0.32.3", | |
179 "type": "tool", | |
180 "uuid": "4f06f828-b69d-4072-bc5e-cbc28a565e2c", | |
181 "workflow_outputs": [] | |
182 }, | |
183 "5": { | |
184 "annotation": "{\n\"accepted_hits\": {\n\"name\": \"tophat_accepted_hits\", \"description\": \"\",\n\"type\": \"bam\"\n}\n}", | |
185 "content_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", | |
186 "id": 5, | |
187 "input_connections": { | |
188 "singlePaired|input1": { | |
189 "id": 4, | |
190 "output_name": "fastq_out_r1_paired" | |
191 }, | |
192 "singlePaired|input2": { | |
193 "id": 4, | |
194 "output_name": "fastq_out_r2_paired" | |
195 } | |
196 }, | |
197 "inputs": [], | |
198 "label": null, | |
199 "name": "TopHat", | |
200 "outputs": [ | |
201 { | |
202 "name": "align_summary", | |
203 "type": "txt" | |
204 }, | |
205 { | |
206 "name": "fusions", | |
207 "type": "tabular" | |
208 }, | |
209 { | |
210 "name": "insertions", | |
211 "type": "bed" | |
212 }, | |
213 { | |
214 "name": "deletions", | |
215 "type": "bed" | |
216 }, | |
217 { | |
218 "name": "junctions", | |
219 "type": "bed" | |
220 }, | |
221 { | |
222 "name": "accepted_hits", | |
223 "type": "bam" | |
224 }, | |
225 { | |
226 "name": "unmapped", | |
227 "type": "bam" | |
228 } | |
229 ], | |
230 "position": { | |
231 "left": 1141, | |
232 "top": 279 | |
233 }, | |
234 "post_job_actions": {}, | |
235 "tool_errors": null, | |
236 "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0", | |
237 "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 2}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"output_unmapped\\\": \\\"False\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": \\\"hg19_genes.gtf\\\", \\\"use_annotations\\\": \\\"indexed\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\"}", | |
238 "tool_version": "2.1.0", | |
239 "type": "tool", | |
240 "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", | |
241 "workflow_outputs": [] | |
242 }, | |
243 "6": { | |
244 "annotation": "{\n\"output\": {\n\"name\": \"feature_counts\", \"description\": \"\",\n\"type\": \"tabular\"\n},\n\"output_summary\": {\n\"name\": \"feature_counts_summary\", \"description\": \"\",\n\"type\": \"tabular\"\n}\n}", | |
245 "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", | |
246 "id": 6, | |
247 "input_connections": { | |
248 "alignments": { | |
249 "id": 5, | |
250 "output_name": "accepted_hits" | |
251 } | |
252 }, | |
253 "inputs": [], | |
254 "label": null, | |
255 "name": "featureCounts", | |
256 "outputs": [ | |
257 { | |
258 "name": "output", | |
259 "type": "tabular" | |
260 }, | |
261 { | |
262 "name": "output_summary", | |
263 "type": "tabular" | |
264 } | |
265 ], | |
266 "position": { | |
267 "left": 1441, | |
268 "top": 388 | |
269 }, | |
270 "post_job_actions": {}, | |
271 "tool_errors": null, | |
272 "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", | |
273 "tool_state": "{\"__page__\": 0, \"reference_gene_sets_source\": \"{\\\"reference_gene_sets\\\": \\\"/mnt/galaxyIndices/gene_annotations/hg19_genes.gtf\\\", \\\"__current_case__\\\": 2, \\\"source_select\\\": \\\"indexed_all\\\"}\", \"format\": \"\\\"tabdel_short\\\"\", \"__rerun_remap_job_id__\": null, \"alignments\": \"null\", \"extended_parameters\": \"{\\\"parameters\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}", | |
274 "tool_version": "1.4.6.p5", | |
275 "type": "tool", | |
276 "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", | |
277 "workflow_outputs": [] | |
278 } | |
279 }, | |
280 "uuid": "3688391c-e028-4483-94a2-c70422e5ffdb" | |
281 } |