annotate 2_BAM_files_TO_clustered_Heatmap_of_read_coverages.ga @ 0:16fc7f46ee23 draft default tip

Uploaded
author bgruening
date Thu, 03 Apr 2014 11:11:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
1 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
2 "a_galaxy_workflow": "true",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
3 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
4 "format-version": "0.1",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
5 "name": "2 BAM files -->(clustered) Heatmap of read coverages",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
6 "steps": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
7 "0": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
8 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
9 "id": 0,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
10 "input_connections": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
11 "inputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
12 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
13 "description": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
14 "name": "file 1 of mapped reads, e.g. treated sample"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
15 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
16 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
17 "name": "Input dataset",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
18 "outputs": [],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
19 "position": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
20 "left": 181.5,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
21 "top": 459
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
22 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
23 "tool_errors": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
24 "tool_id": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
25 "tool_state": "{\"name\": \"file 1 of mapped reads, e.g. treated sample\"}",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
26 "tool_version": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
27 "type": "data_input",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
28 "user_outputs": []
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
29 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
30 "1": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
31 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
32 "id": 1,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
33 "input_connections": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
34 "inputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
35 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
36 "description": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
37 "name": "file 2 of mapped reads, e.g. control sample"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
38 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
39 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
40 "name": "Input dataset",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
41 "outputs": [],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
42 "position": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
43 "left": 183.5,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
44 "top": 573
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
45 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
46 "tool_errors": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
47 "tool_id": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
48 "tool_state": "{\"name\": \"file 2 of mapped reads, e.g. control sample\"}",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
49 "tool_version": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
50 "type": "data_input",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
51 "user_outputs": []
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
52 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
53 "2": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
54 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
55 "id": 2,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
56 "input_connections": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
57 "inputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
58 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
59 "description": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
60 "name": "regions"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
61 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
62 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
63 "name": "Input dataset",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
64 "outputs": [],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
65 "position": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
66 "left": 598.5,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
67 "top": 397.5
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
68 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
69 "tool_errors": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
70 "tool_id": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
71 "tool_state": "{\"name\": \"regions\"}",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
72 "tool_version": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
73 "type": "data_input",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
74 "user_outputs": []
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
75 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
76 "3": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
77 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
78 "id": 3,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
79 "input_connections": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
80 "bamFile1": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
81 "id": 0,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
82 "output_name": "output"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
83 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
84 "bamFile2": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
85 "id": 1,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
86 "output_name": "output"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
87 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
88 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
89 "inputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
90 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
91 "description": "runtime parameter for tool bamCompare",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
92 "name": "region"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
93 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
94 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
95 "description": "runtime parameter for tool bamCompare",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
96 "name": "advancedOpt"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
97 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
98 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
99 "description": "runtime parameter for tool bamCompare",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
100 "name": "fragmentLength"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
101 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
102 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
103 "name": "bamCompare",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
104 "outputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
105 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
106 "name": "outFileName",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
107 "type": "bigwig"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
108 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
109 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
110 "position": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
111 "left": 479.5,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
112 "top": 488.5
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
113 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
114 "post_job_actions": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
115 "HideDatasetActionoutFileName": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
116 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
117 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
118 "output_name": "outFileName"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
119 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
120 "RenameDatasetActionoutFileName": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
121 "action_arguments": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
122 "newname": "BAM1_vs_BAM2_log2ratio.bigwig"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
123 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
124 "action_type": "RenameDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
125 "output_name": "outFileName"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
126 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
127 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
128 "tool_errors": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
129 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCompare/1.1.0",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
130 "tool_state": "{\"comparison\": \"{\\\"type\\\": \\\"log2\\\", \\\"__current_case__\\\": 0}\", \"bamFile2\": \"null\", \"outFileFormat\": \"\\\"bigwig\\\"\", \"bamFile1\": \"null\", \"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"binSize\": \"\\\"50\\\"\", \"scaling\": \"{\\\"method\\\": \\\"readCount\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advancedOpt\": \"{\\\"ignoreDuplicates\\\": \\\"True\\\", \\\"ignoreForNormalization\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"doNotExtendPairedEnds\\\": \\\"False\\\", \\\"missingDataAsZero\\\": \\\"True\\\", \\\"smoothLength\\\": \\\"150\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"minMappingQuality\\\": \\\"10\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
131 "tool_version": "1.1.0",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
132 "type": "tool",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
133 "user_outputs": []
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
134 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
135 "4": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
136 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
137 "id": 4,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
138 "input_connections": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
139 "regionsFiles_0|regionsFile": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
140 "id": 2,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
141 "output_name": "output"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
142 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
143 "scoreFile": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
144 "id": 3,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
145 "output_name": "outFileName"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
146 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
147 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
148 "inputs": [],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
149 "name": "computeMatrix",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
150 "outputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
151 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
152 "name": "outFileName",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
153 "type": "bgzip"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
154 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
155 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
156 "name": "outFileNameData",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
157 "type": "tabular"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
158 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
159 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
160 "name": "outFileSortedRegions",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
161 "type": "bed"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
162 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
163 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
164 "name": "outFileNameMatrix",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
165 "type": "tabular"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
166 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
167 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
168 "position": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
169 "left": 838.61669921875,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
170 "top": 366.1166687011719
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
171 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
172 "post_job_actions": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
173 "HideDatasetActionoutFileNameData": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
174 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
175 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
176 "output_name": "outFileNameData"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
177 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
178 "HideDatasetActionoutFileNameMatrix": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
179 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
180 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
181 "output_name": "outFileNameMatrix"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
182 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
183 "HideDatasetActionoutFileSortedRegions": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
184 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
185 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
186 "output_name": "outFileSortedRegions"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
187 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
188 "RenameDatasetActionoutFileName": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
189 "action_arguments": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
190 "newname": "computeMatrix: matrix of coverage values for BED file"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
191 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
192 "action_type": "RenameDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
193 "output_name": "outFileName"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
194 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
195 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
196 "tool_errors": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
197 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.1.0",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
198 "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"startLabel\\\": \\\"TSS\\\", \\\"regionStartLength\\\": {\\\"afterRegionStartLength\\\": \\\"1000\\\", \\\"regionStartLength_select\\\": \\\"yes\\\", \\\"beforeRegionStartLength\\\": \\\"1000\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"endLabel\\\": \\\"TES\\\", \\\"regionBodyLength\\\": \\\"2000\\\", \\\"mode_select\\\": \\\"scale-regions\\\"}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\"}",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
199 "tool_version": "1.1.0",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
200 "type": "tool",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
201 "user_outputs": []
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
202 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
203 "5": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
204 "annotation": "",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
205 "id": 5,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
206 "input_connections": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
207 "matrixFile": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
208 "id": 4,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
209 "output_name": "outFileName"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
210 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
211 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
212 "inputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
213 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
214 "description": "runtime parameter for tool heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
215 "name": "output"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
216 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
217 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
218 "description": "runtime parameter for tool heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
219 "name": "advancedOpt"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
220 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
221 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
222 "description": "runtime parameter for tool heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
223 "name": "advancedOpt"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
224 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
225 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
226 "description": "runtime parameter for tool heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
227 "name": "advancedOpt"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
228 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
229 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
230 "description": "runtime parameter for tool heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
231 "name": "advancedOpt"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
232 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
233 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
234 "description": "runtime parameter for tool heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
235 "name": "advancedOpt"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
236 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
237 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
238 "name": "heatmapper",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
239 "outputs": [
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
240 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
241 "name": "outFileName",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
242 "type": "png"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
243 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
244 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
245 "name": "outFileNameData",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
246 "type": "tabular"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
247 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
248 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
249 "name": "outFileSortedRegions",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
250 "type": "bed"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
251 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
252 {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
253 "name": "outFileNameMatrix",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
254 "type": "tabular"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
255 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
256 ],
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
257 "position": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
258 "left": 1147.5,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
259 "top": 399
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
260 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
261 "post_job_actions": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
262 "HideDatasetActionoutFileNameData": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
263 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
264 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
265 "output_name": "outFileNameData"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
266 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
267 "HideDatasetActionoutFileNameMatrix": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
268 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
269 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
270 "output_name": "outFileNameMatrix"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
271 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
272 "HideDatasetActionoutFileSortedRegions": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
273 "action_arguments": {},
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
274 "action_type": "HideDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
275 "output_name": "outFileSortedRegions"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
276 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
277 "RenameDatasetActionoutFileName": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
278 "action_arguments": {
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
279 "newname": "Heatmap of BAM1_BAM2_log2ratios"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
280 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
281 "action_type": "RenameDatasetAction",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
282 "output_name": "outFileName"
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
283 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
284 },
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
285 "tool_errors": null,
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
286 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.1.0",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
287 "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"xAxisLabel\\\": \\\"\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
288 "tool_version": "1.1.0",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
289 "type": "tool",
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
290 "user_outputs": []
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
291 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
292 }
16fc7f46ee23 Uploaded
bgruening
parents:
diff changeset
293 }