annotate Kallisto_RNA-seq_(PE)_Quantification_-_Mouse.ga @ 1:cbf8233bf744 draft default tip

planemo upload commit dc4a5924dc98d22c14eac246506d13dfc13c3c6d
author scottx611x
date Tue, 04 Sep 2018 15:12:04 -0400
parents ce9f11c6b94b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
1 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
2 "a_galaxy_workflow": "true",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
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}",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
4 "format-version": "0.1",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
5 "name": "Kallisto RNA-seq (PE) Quantification - Mouse",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
6 "steps": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
7 "0": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
8 "annotation": "",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
9 "content_id": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
10 "errors": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
11 "id": 0,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
12 "input_connections": {},
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
13 "inputs": [],
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
14 "label": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
15 "name": "Input dataset collection",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
16 "outputs": [],
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
17 "position": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
18 "left": 577.5,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
19 "top": 309
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
20 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
21 "tool_id": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
22 "tool_state": "{\"collection_type\": \"list:paired\"}",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
23 "tool_version": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
24 "type": "data_collection_input",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
25 "uuid": "114f35e8-a538-4978-80ad-786750f2e65a",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
26 "workflow_outputs": [
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
27 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
28 "label": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
29 "output_name": "output",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
30 "uuid": "8ca3b6da-cc1e-46b3-a475-6abb4230528c"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
31 }
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
32 ]
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
33 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
34 "1": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
35 "annotation": "",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
36 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
37 "errors": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
38 "id": 1,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
39 "input_connections": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
40 "single_paired|collection|reads": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
41 "id": 0,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
42 "output_name": "output"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
43 }
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
44 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
45 "inputs": [],
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
46 "label": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
47 "name": "Kallisto quant",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
48 "outputs": [
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
49 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
50 "name": "abundance_h5",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
51 "type": "h5"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
52 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
53 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
54 "name": "abundance_tab",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
55 "type": "tabular"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
56 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
57 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
58 "name": "pseudobam_output",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
59 "type": "bam"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
60 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
61 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
62 "name": "fusion_output",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
63 "type": "tabular"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
64 }
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
65 ],
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
66 "position": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
67 "left": 964,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
68 "top": 328.5
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
69 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
70 "post_job_actions": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
71 "HideDatasetActionabundance_h5": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
72 "action_arguments": {},
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
73 "action_type": "HideDatasetAction",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
74 "output_name": "abundance_h5"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
75 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
76 "HideDatasetActionfusion_output": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
77 "action_arguments": {},
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
78 "action_type": "HideDatasetAction",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
79 "output_name": "fusion_output"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
80 }
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
81 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
82 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
83 "tool_shed_repository": {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
84 "changeset_revision": "b818b23df1e0",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
85 "name": "kallisto_quant",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
86 "owner": "iuc",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
87 "tool_shed": "toolshed.g2.bx.psu.edu"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
88 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
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\\\"\"}",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
90 "tool_version": "0.43.1.3",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
91 "type": "tool",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
92 "uuid": "42dbc102-33eb-4c40-a927-21d782c98f25",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
93 "workflow_outputs": [
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
94 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
95 "label": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
96 "output_name": "pseudobam_output",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
97 "uuid": "44ce1fa6-a045-4f45-b356-ab65f6ad05c8"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
98 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
99 {
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
100 "label": null,
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
101 "output_name": "abundance_tab",
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
102 "uuid": "2136144c-08f2-4fae-8937-b1c99a5d7f52"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
103 }
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
104 ]
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
105 }
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
106 },
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
107 "uuid": "00c71013-84ba-4eb1-b42b-d57dc0dc9dea"
ce9f11c6b94b planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
scottx611x
parents:
diff changeset
108 }