comparison RNA-seq_(PE)_Quantification_-_Human.ga @ 2:324f32e70ea4 draft default tip

Update annotations
author stemcellcommons
date Wed, 25 Oct 2017 15:10:22 -0400
parents
children
comparison
equal deleted inserted replaced
1:ba1b76257fa5 2:324f32e70ea4
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "{\n\t\"description\": \"Transcript quantification for paired-end RNA-seq data. Reads are aligned to the human (hg19) reference genome.\",\n\t\"file_relationship\": {\n\t\t\"value_type\": \"LIST\",\n\t\t\"name\": \"List of Paired inputs\",\n\t\t\"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired FASTQ files\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Forward FASTQ\",\n\t\t\t\t\t\"description\": \"Forward FASTQ\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Reverse FASTQ\",\n\t\t\t\t\t\"description\": \"Reverse FASTQ\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}",
4 "format-version": "0.1",
5 "name": "RNA-seq (PE) Quantification - Human",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "id": 0,
11 "input_connections": {},
12 "inputs": [
13 {
14 "description": "",
15 "name": "Input Dataset Collection"
16 }
17 ],
18 "label": null,
19 "name": "Input dataset collection",
20 "outputs": [],
21 "position": {
22 "left": 200,
23 "top": 321.5
24 },
25 "tool_errors": null,
26 "tool_id": null,
27 "tool_state": "{\"collection_type\": \"paired\", \"name\": \"Input Dataset Collection\"}",
28 "tool_version": null,
29 "type": "data_collection_input",
30 "uuid": "24dc08ea-da03-43f1-80e1-00321e037d6e",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "7787dd38-db4e-4f45-8f3e-b75f038257c7"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
42 "id": 1,
43 "input_connections": {
44 "input_collection": {
45 "id": 0,
46 "output_name": "output"
47 }
48 },
49 "inputs": [],
50 "label": null,
51 "name": "Split Paired Collection",
52 "outputs": [
53 {
54 "name": "forward_element",
55 "type": "data"
56 },
57 {
58 "name": "reverse_element",
59 "type": "data"
60 }
61 ],
62 "position": {
63 "left": 503,
64 "top": 349.5
65 },
66 "post_job_actions": {
67 "ChangeDatatypeActionforward_element": {
68 "action_arguments": {
69 "newtype": "fastqsanger"
70 },
71 "action_type": "ChangeDatatypeAction",
72 "output_name": "forward_element"
73 },
74 "ChangeDatatypeActionreverse_element": {
75 "action_arguments": {
76 "newtype": "fastqsanger"
77 },
78 "action_type": "ChangeDatatypeAction",
79 "output_name": "reverse_element"
80 },
81 "HideDatasetActionforward_element": {
82 "action_arguments": {},
83 "action_type": "HideDatasetAction",
84 "output_name": "forward_element"
85 },
86 "HideDatasetActionreverse_element": {
87 "action_arguments": {},
88 "action_type": "HideDatasetAction",
89 "output_name": "reverse_element"
90 }
91 },
92 "tool_errors": null,
93 "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
94 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_collection\": \"null\"}",
95 "tool_version": "0.2",
96 "type": "tool",
97 "uuid": "a7bd61cc-00d1-4666-b0eb-c3b119944c1d",
98 "workflow_outputs": []
99 },
100 "2": {
101 "annotation": "",
102 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
103 "id": 2,
104 "input_connections": {
105 "input_file": {
106 "id": 1,
107 "output_name": "forward_element"
108 }
109 },
110 "inputs": [],
111 "label": null,
112 "name": "FASTQ Parallel Groomer",
113 "outputs": [
114 {
115 "name": "output_file",
116 "type": "fastqsanger"
117 }
118 ],
119 "position": {
120 "left": 852,
121 "top": 251
122 },
123 "post_job_actions": {
124 "HideDatasetActionoutput_file": {
125 "action_arguments": {},
126 "action_type": "HideDatasetAction",
127 "output_name": "output_file"
128 }
129 },
130 "tool_errors": null,
131 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
132 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
133 "tool_version": "0.3.1",
134 "type": "tool",
135 "uuid": "cde46b5a-7a85-4408-b715-3221a0ecf4f3",
136 "workflow_outputs": []
137 },
138 "3": {
139 "annotation": "",
140 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
141 "id": 3,
142 "input_connections": {
143 "input_file": {
144 "id": 1,
145 "output_name": "reverse_element"
146 }
147 },
148 "inputs": [],
149 "label": null,
150 "name": "FASTQ Parallel Groomer",
151 "outputs": [
152 {
153 "name": "output_file",
154 "type": "fastqsanger"
155 }
156 ],
157 "position": {
158 "left": 853,
159 "top": 422
160 },
161 "post_job_actions": {
162 "HideDatasetActionoutput_file": {
163 "action_arguments": {},
164 "action_type": "HideDatasetAction",
165 "output_name": "output_file"
166 }
167 },
168 "tool_errors": null,
169 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
170 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
171 "tool_version": "0.3.1",
172 "type": "tool",
173 "uuid": "24b5c72c-64a5-40a3-826b-5ca963508597",
174 "workflow_outputs": []
175 },
176 "4": {
177 "annotation": "",
178 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
179 "id": 4,
180 "input_connections": {
181 "paired_end|paired_input_type_conditional|fastq_r1_in": {
182 "id": 2,
183 "output_name": "output_file"
184 },
185 "paired_end|paired_input_type_conditional|fastq_r2_in": {
186 "id": 3,
187 "output_name": "output_file"
188 }
189 },
190 "inputs": [],
191 "label": null,
192 "name": "Trimmomatic",
193 "outputs": [
194 {
195 "name": "fastq_out_paired",
196 "type": "input"
197 },
198 {
199 "name": "fastq_out_unpaired",
200 "type": "input"
201 },
202 {
203 "name": "fastq_out_r1_paired",
204 "type": "fastqsanger"
205 },
206 {
207 "name": "fastq_out_r2_paired",
208 "type": "fastqsanger"
209 },
210 {
211 "name": "fastq_out_r1_unpaired",
212 "type": "fastqsanger"
213 },
214 {
215 "name": "fastq_out_r2_unpaired",
216 "type": "fastqsanger"
217 },
218 {
219 "name": "fastq_out",
220 "type": "fastqsanger"
221 }
222 ],
223 "position": {
224 "left": 1211.5,
225 "top": 292
226 },
227 "post_job_actions": {
228 "HideDatasetActionfastq_out": {
229 "action_arguments": {},
230 "action_type": "HideDatasetAction",
231 "output_name": "fastq_out"
232 },
233 "HideDatasetActionfastq_out_paired": {
234 "action_arguments": {},
235 "action_type": "HideDatasetAction",
236 "output_name": "fastq_out_paired"
237 },
238 "HideDatasetActionfastq_out_r1_paired": {
239 "action_arguments": {},
240 "action_type": "HideDatasetAction",
241 "output_name": "fastq_out_r1_paired"
242 },
243 "HideDatasetActionfastq_out_r1_unpaired": {
244 "action_arguments": {},
245 "action_type": "HideDatasetAction",
246 "output_name": "fastq_out_r1_unpaired"
247 },
248 "HideDatasetActionfastq_out_r2_paired": {
249 "action_arguments": {},
250 "action_type": "HideDatasetAction",
251 "output_name": "fastq_out_r2_paired"
252 },
253 "HideDatasetActionfastq_out_r2_unpaired": {
254 "action_arguments": {},
255 "action_type": "HideDatasetAction",
256 "output_name": "fastq_out_r2_unpaired"
257 },
258 "HideDatasetActionfastq_out_unpaired": {
259 "action_arguments": {},
260 "action_type": "HideDatasetAction",
261 "output_name": "fastq_out_unpaired"
262 }
263 },
264 "tool_errors": null,
265 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
266 "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\\\"}\"}",
267 "tool_version": "0.32.3",
268 "type": "tool",
269 "uuid": "c60a6cd7-6121-42c2-abff-f5d391b87d40",
270 "workflow_outputs": []
271 },
272 "5": {
273 "annotation": "{\n\"accepted_hits\": {\n\"name\": \"tophat_accepted_hits\", \"description\": \"\",\n\"type\": \"bam\"\n}\n}",
274 "content_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0",
275 "id": 5,
276 "input_connections": {
277 "singlePaired|input1": {
278 "id": 4,
279 "output_name": "fastq_out_r1_paired"
280 },
281 "singlePaired|input2": {
282 "id": 4,
283 "output_name": "fastq_out_r2_paired"
284 }
285 },
286 "inputs": [],
287 "label": null,
288 "name": "TopHat",
289 "outputs": [
290 {
291 "name": "align_summary",
292 "type": "txt"
293 },
294 {
295 "name": "fusions",
296 "type": "tabular"
297 },
298 {
299 "name": "insertions",
300 "type": "bed"
301 },
302 {
303 "name": "deletions",
304 "type": "bed"
305 },
306 {
307 "name": "junctions",
308 "type": "bed"
309 },
310 {
311 "name": "accepted_hits",
312 "type": "bam"
313 },
314 {
315 "name": "unmapped",
316 "type": "bam"
317 }
318 ],
319 "position": {
320 "left": 1561.5,
321 "top": 289
322 },
323 "post_job_actions": {
324 "HideDatasetActionalign_summary": {
325 "action_arguments": {},
326 "action_type": "HideDatasetAction",
327 "output_name": "align_summary"
328 },
329 "HideDatasetActiondeletions": {
330 "action_arguments": {},
331 "action_type": "HideDatasetAction",
332 "output_name": "deletions"
333 },
334 "HideDatasetActionfusions": {
335 "action_arguments": {},
336 "action_type": "HideDatasetAction",
337 "output_name": "fusions"
338 },
339 "HideDatasetActioninsertions": {
340 "action_arguments": {},
341 "action_type": "HideDatasetAction",
342 "output_name": "insertions"
343 },
344 "HideDatasetActionjunctions": {
345 "action_arguments": {},
346 "action_type": "HideDatasetAction",
347 "output_name": "junctions"
348 },
349 "HideDatasetActionunmapped": {
350 "action_arguments": {},
351 "action_type": "HideDatasetAction",
352 "output_name": "unmapped"
353 }
354 },
355 "tool_errors": null,
356 "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0",
357 "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}\"}",
358 "tool_version": "2.1.0",
359 "type": "tool",
360 "uuid": "24e4d439-89ab-4f92-be42-08ef5b3702c4",
361 "workflow_outputs": [
362 {
363 "label": null,
364 "output_name": "accepted_hits",
365 "uuid": "afbf0ed7-39a7-4eaf-8f26-8ea1b550b2ec"
366 }
367 ]
368 },
369 "6": {
370 "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}",
371 "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5",
372 "id": 6,
373 "input_connections": {
374 "alignments": {
375 "id": 5,
376 "output_name": "accepted_hits"
377 }
378 },
379 "inputs": [],
380 "label": null,
381 "name": "featureCounts",
382 "outputs": [
383 {
384 "name": "output",
385 "type": "tabular"
386 },
387 {
388 "name": "output_summary",
389 "type": "tabular"
390 }
391 ],
392 "position": {
393 "left": 1861.5,
394 "top": 398
395 },
396 "post_job_actions": {},
397 "tool_errors": null,
398 "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5",
399 "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}\"}",
400 "tool_version": "1.4.6.p5",
401 "type": "tool",
402 "uuid": "f3e95bbb-f1dd-4d97-9ea3-ec90ee2b9ab8",
403 "workflow_outputs": [
404 {
405 "label": null,
406 "output_name": "output_summary",
407 "uuid": "9162a69c-9023-4ab4-9931-2e147e02f1f4"
408 },
409 {
410 "label": null,
411 "output_name": "output",
412 "uuid": "772073ae-2b57-4dda-bf6e-c8725c01b106"
413 }
414 ]
415 }
416 },
417 "uuid": "a5618acc-41ea-45c2-9cf2-f8ebd7463d88"
418 }