Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
comparison Kallisto_RNA-seq_(PE)_Quantification_-_Mouse.ga @ 0:ce9f11c6b94b draft
planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author | scottx611x |
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date | Tue, 04 Sep 2018 13:56:11 -0400 |
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-1:000000000000 | 0:ce9f11c6b94b |
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1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "{\n \"description\": \"Rapid transcript quantification via pseudoalignment (https://pachterlab.github.io/kallisto/). Paired-end reads are quantified against the mm10 transcriptome.\",\n \"file_relationship\": {\n \"value_type\": \"LIST\",\n \"name\": \"List of Read Pairs\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"PAIR\",\n \"name\": \"Read Pair\",\n \"input_files\": [{\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}],\n \"name\": \"Input File\",\n \"description\": \"Forward Reads\"\n },\n {\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}],\n \"name\": \"Input File\",\n \"description\": \"Reverse Reads\"\n }\n ]\n }\n }\n}", | |
4 "format-version": "0.1", | |
5 "name": "Kallisto RNA-seq (PE) Quantification - Mouse", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "content_id": null, | |
10 "errors": null, | |
11 "id": 0, | |
12 "input_connections": {}, | |
13 "inputs": [], | |
14 "label": null, | |
15 "name": "Input dataset collection", | |
16 "outputs": [], | |
17 "position": { | |
18 "left": 577.5, | |
19 "top": 309 | |
20 }, | |
21 "tool_id": null, | |
22 "tool_state": "{\"collection_type\": \"list:paired\"}", | |
23 "tool_version": null, | |
24 "type": "data_collection_input", | |
25 "uuid": "114f35e8-a538-4978-80ad-786750f2e65a", | |
26 "workflow_outputs": [ | |
27 { | |
28 "label": null, | |
29 "output_name": "output", | |
30 "uuid": "8ca3b6da-cc1e-46b3-a475-6abb4230528c" | |
31 } | |
32 ] | |
33 }, | |
34 "1": { | |
35 "annotation": "", | |
36 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", | |
37 "errors": null, | |
38 "id": 1, | |
39 "input_connections": { | |
40 "single_paired|collection|reads": { | |
41 "id": 0, | |
42 "output_name": "output" | |
43 } | |
44 }, | |
45 "inputs": [], | |
46 "label": null, | |
47 "name": "Kallisto quant", | |
48 "outputs": [ | |
49 { | |
50 "name": "abundance_h5", | |
51 "type": "h5" | |
52 }, | |
53 { | |
54 "name": "abundance_tab", | |
55 "type": "tabular" | |
56 }, | |
57 { | |
58 "name": "pseudobam_output", | |
59 "type": "bam" | |
60 }, | |
61 { | |
62 "name": "fusion_output", | |
63 "type": "tabular" | |
64 } | |
65 ], | |
66 "position": { | |
67 "left": 964, | |
68 "top": 328.5 | |
69 }, | |
70 "post_job_actions": { | |
71 "HideDatasetActionabundance_h5": { | |
72 "action_arguments": {}, | |
73 "action_type": "HideDatasetAction", | |
74 "output_name": "abundance_h5" | |
75 }, | |
76 "HideDatasetActionfusion_output": { | |
77 "action_arguments": {}, | |
78 "action_type": "HideDatasetAction", | |
79 "output_name": "fusion_output" | |
80 } | |
81 }, | |
82 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", | |
83 "tool_shed_repository": { | |
84 "changeset_revision": "b818b23df1e0", | |
85 "name": "kallisto_quant", | |
86 "owner": "iuc", | |
87 "tool_shed": "toolshed.g2.bx.psu.edu" | |
88 }, | |
89 "tool_state": "{\"__page__\": null, \"bootstrap_samples\": \"\\\"0\\\"\", \"single_paired\": \"{\\\"collection\\\": {\\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"collection_selector\\\": \\\"collection\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"single_paired_selector\\\": \\\"paired\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_transcriptome\": \"{\\\"index\\\": \\\"mm10\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", | |
90 "tool_version": "0.43.1.3", | |
91 "type": "tool", | |
92 "uuid": "42dbc102-33eb-4c40-a927-21d782c98f25", | |
93 "workflow_outputs": [ | |
94 { | |
95 "label": null, | |
96 "output_name": "pseudobam_output", | |
97 "uuid": "44ce1fa6-a045-4f45-b356-ab65f6ad05c8" | |
98 }, | |
99 { | |
100 "label": null, | |
101 "output_name": "abundance_tab", | |
102 "uuid": "2136144c-08f2-4fae-8937-b1c99a5d7f52" | |
103 } | |
104 ] | |
105 } | |
106 }, | |
107 "uuid": "00c71013-84ba-4eb1-b42b-d57dc0dc9dea" | |
108 } |