Mercurial > repos > stemcellcommons > deeptools_bamqc_workflow

comparison deepTools_BAM_QC.ga @ 0:897b11a77250 draft default tip

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planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author scottx611x
date Tue, 04 Sep 2018 13:55:35 -0400
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-1:000000000000 0:897b11a77250
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "{ \n \"description\": \"Compare aligned samples via pairwise correlation heatmap and PCA plot\", \n \"file_relationship\": { \n \"file_relationship\": {}, \n \"value_type\": \"LIST\", \n \"name\": \"List of BAM Files\", \n \"input_files\": [ \n { \n \"allowed_filetypes\": [{\"name\": \"BAM\"}], \n \"name\": \"Input File\", \n \"description\": \"File to run deepTools BAM QC on\" \n } \n ] \n } \n}",
4 "format-version": "0.1",
5 "name": "deepTools BAM QC",
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": {
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19 "top": 287.5
20 },
21 "tool_id": null,
22 "tool_state": "{\"collection_type\": \"list\"}",
23 "tool_version": null,
24 "type": "data_collection_input",
25 "uuid": "7e26711f-78ba-4f74-90ea-b30acefcf685",
26 "workflow_outputs": [
27 {
28 "label": null,
29 "output_name": "output",
30 "uuid": "ef8c102b-e5a8-4a1e-9bbc-cf875cfcd72e"
31 }
32 ]
33 },
34 "1": {
35 "annotation": "",
36 "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0",
37 "errors": null,
38 "id": 1,
39 "input_connections": {
40 "bamfiles": {
41 "id": 0,
42 "output_name": "output"
43 }
44 },
45 "inputs": [
46 {
47 "description": "runtime parameter for tool multiBamSummary",
48 "name": "bamfiles"
49 }
50 ],
51 "label": null,
52 "name": "multiBamSummary",
53 "outputs": [
54 {
55 "name": "outFile",
56 "type": "deeptools_coverage_matrix"
57 },
58 {
59 "name": "outFileRawCounts",
60 "type": "tabular"
61 }
62 ],
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66 },
67 "post_job_actions": {},
68 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0",
69 "tool_shed_repository": {
70 "changeset_revision": "87d2c75884d9",
71 "name": "deeptools_multi_bam_summary",
72 "owner": "bgruening",
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74 },
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76 "tool_version": "2.2.3.0",
77 "type": "tool",
78 "uuid": "b199cca5-5101-4ad0-8f17-aa902c5ece8f",
79 "workflow_outputs": [
80 {
81 "label": null,
82 "output_name": "outFileRawCounts",
83 "uuid": "90b33467-e9cc-4c8a-8e96-f8c12c1a8daf"
84 },
85 {
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87 "output_name": "outFile",
88 "uuid": "fe5ce046-edd4-4953-8b20-4ccabb4d6eb2"
89 }
90 ]
91 },
92 "2": {
93 "annotation": "",
94 "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0",
95 "errors": null,
96 "id": 2,
97 "input_connections": {
98 "corData": {
99 "id": 1,
100 "output_name": "outFile"
101 }
102 },
103 "inputs": [
104 {
105 "description": "runtime parameter for tool plotCorrelation",
106 "name": "corData"
107 }
108 ],
109 "label": null,
110 "name": "plotCorrelation",
111 "outputs": [
112 {
113 "name": "outFileName",
114 "type": "png"
115 },
116 {
117 "name": "matrix",
118 "type": "tabular"
119 }
120 ],
121 "position": {
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124 },
125 "post_job_actions": {},
126 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0",
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129 "name": "deeptools_plot_correlation",
130 "owner": "bgruening",
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132 },
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134 "tool_version": "2.2.3.0",
135 "type": "tool",
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137 "workflow_outputs": [
138 {
139 "label": null,
140 "output_name": "outFileName",
141 "uuid": "04d6ff82-6f3c-4bb8-8449-5c212a152aa3"
142 },
143 {
144 "label": null,
145 "output_name": "matrix",
146 "uuid": "94a22779-d526-4fb0-aae1-ad8c36cb6ffc"
147 }
148 ]
149 },
150 "3": {
151 "annotation": "",
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158 "output_name": "outFile"
159 }
160 },
161 "inputs": [
162 {
163 "description": "runtime parameter for tool plotPCA",
164 "name": "corData"
165 }
166 ],
167 "label": null,
168 "name": "plotPCA",
169 "outputs": [
170 {
171 "name": "outFileName",
172 "type": "png"
173 },
174 {
175 "name": "output_outFileNameData",
176 "type": "tabular"
177 }
178 ],
179 "position": {
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182 },
183 "post_job_actions": {},
184 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0",
185 "tool_shed_repository": {
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187 "name": "deeptools_plot_pca",
188 "owner": "bgruening",
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190 },
191 "tool_state": "{\"__page__\": null, \"plotTitle\": \"\\\"\\\"\", \"outFileFormat\": \"\\\"png\\\"\", \"__rerun_remap_job_id__\": null, \"outFileNameData\": \"\\\"false\\\"\", \"corData\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
192 "tool_version": "2.2.3.0",
193 "type": "tool",
194 "uuid": "4a7bf483-9e9e-4c4d-bd87-f4b3ddbaa83f",
195 "workflow_outputs": [
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210 }