Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows

comparison Kallisto_RNA-seq_(PE)_Quantification_-_Zebrafish.ga @ 0:ce9f11c6b94b draft

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planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author scottx611x
date Tue, 04 Sep 2018 13:56:11 -0400
parents
children cbf8233bf744
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-1:000000000000 0:ce9f11c6b94b
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 danRer11 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 - Human",
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": 366.5,
19 "top": 295
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": "f906db26-f882-4e34-a638-74fe8aa56523"
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": 796,
68 "top": 327.5
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\\\": \\\"hg38\\\", \\\"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": "df9dd3c7-028a-4b96-a09c-33bbb14db527",
93 "workflow_outputs": [
94 {
95 "label": null,
96 "output_name": "pseudobam_output",
97 "uuid": "47d4c13b-218f-4a2b-b116-0516a0a9b109"
98 },
99 {
100 "label": null,
101 "output_name": "abundance_tab",
102 "uuid": "fe306756-a099-4e50-aa1f-6983dfff2d00"
103 }
104 ]
105 }
106 },
107 "uuid": "2ec7af1e-4f59-44a8-99d3-28ceda87411d"
108 }