Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
comparison Kallisto_RNA-seq_(SE)_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/). Single-end reads are quantified against the mm10 transcriptome.\", \n \"file_relationship\": { \n \"file_relationship\": {}, \n \"value_type\": \"LIST\", \n \"name\": \"List of FASTQ Files\", \n \"input_files\": [ \n { \n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}], \n \"name\": \"Input File\", \n \"description\": \"FASTQ File\" \n } \n ] \n } \n}", | |
4 "format-version": "0.1", | |
5 "name": "Kallisto RNA-seq (SE) 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": 372.5, | |
19 "top": 214 | |
20 }, | |
21 "tool_id": null, | |
22 "tool_state": "{\"collection_type\": \"list\"}", | |
23 "tool_version": null, | |
24 "type": "data_collection_input", | |
25 "uuid": "38a1eccd-850d-4b18-876c-097acf776154", | |
26 "workflow_outputs": [ | |
27 { | |
28 "label": null, | |
29 "output_name": "output", | |
30 "uuid": "98278f40-220b-4dea-bd35-f95547c253b0" | |
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|reads": { | |
41 "id": 0, | |
42 "output_name": "output" | |
43 } | |
44 }, | |
45 "inputs": [ | |
46 { | |
47 "description": "runtime parameter for tool Kallisto quant", | |
48 "name": "single_paired" | |
49 } | |
50 ], | |
51 "label": null, | |
52 "name": "Kallisto quant", | |
53 "outputs": [ | |
54 { | |
55 "name": "abundance_h5", | |
56 "type": "h5" | |
57 }, | |
58 { | |
59 "name": "abundance_tab", | |
60 "type": "tabular" | |
61 }, | |
62 { | |
63 "name": "pseudobam_output", | |
64 "type": "bam" | |
65 }, | |
66 { | |
67 "name": "fusion_output", | |
68 "type": "tabular" | |
69 } | |
70 ], | |
71 "position": { | |
72 "left": 874, | |
73 "top": 325.5 | |
74 }, | |
75 "post_job_actions": { | |
76 "HideDatasetActionabundance_h5": { | |
77 "action_arguments": {}, | |
78 "action_type": "HideDatasetAction", | |
79 "output_name": "abundance_h5" | |
80 }, | |
81 "HideDatasetActionabundance_tab": { | |
82 "action_arguments": {}, | |
83 "action_type": "HideDatasetAction", | |
84 "output_name": "abundance_tab" | |
85 }, | |
86 "HideDatasetActionfusion_output": { | |
87 "action_arguments": {}, | |
88 "action_type": "HideDatasetAction", | |
89 "output_name": "fusion_output" | |
90 } | |
91 }, | |
92 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", | |
93 "tool_shed_repository": { | |
94 "changeset_revision": "b818b23df1e0", | |
95 "name": "kallisto_quant", | |
96 "owner": "iuc", | |
97 "tool_shed": "toolshed.g2.bx.psu.edu" | |
98 }, | |
99 "tool_state": "{\"__page__\": null, \"bootstrap_samples\": \"\\\"0\\\"\", \"single_paired\": \"{\\\"fragment_length\\\": \\\"200\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"single_paired_selector\\\": \\\"single\\\", \\\"sd\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_transcriptome\": \"{\\\"index\\\": \\\"mm10\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", | |
100 "tool_version": "0.43.1.3", | |
101 "type": "tool", | |
102 "uuid": "c124061f-5652-4e12-878b-88ecdaf4cc09", | |
103 "workflow_outputs": [ | |
104 { | |
105 "label": null, | |
106 "output_name": "pseudobam_output", | |
107 "uuid": "84016f1d-3195-49ae-8aad-764d3b1d2729" | |
108 } | |
109 ] | |
110 } | |
111 }, | |
112 "uuid": "95467aa5-2868-4f50-a026-7f89be4306a8" | |
113 } |