Mercurial > repos > bgruening > deeptools
comparison Galaxy-Workflow-2_BAM_files_--_(clustered)_Heatmap_of_read_coverages.ga @ 25:d2898b81b912 draft
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author | bgruening |
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date | Tue, 04 Feb 2014 13:45:17 -0500 |
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24:d7c9fd76e41e | 25:d2898b81b912 |
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1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "Normalizes 2 BAM files to each other (log2ratio of BAM-file 1 / BAM file 2). Then generates a heatmap for regions supplied in 1 BED file (clustering possible). Output: bigWig file, computeMatrix table, heatmapper image", | |
4 "format-version": "0.1", | |
5 "name": "2 BAM files -->(clustered) Heatmap of read coverages", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "sorted BAM file", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "sorted BAM file", | |
14 "name": "file 1 of mapped reads, e.g. treated sample" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
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22 }, | |
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24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"file 1 of mapped reads, e.g. treated sample\"}", | |
26 "tool_version": null, | |
27 "type": "data_input", | |
28 "user_outputs": [] | |
29 }, | |
30 "1": { | |
31 "annotation": "BED or INTERVAL file of genome regions to plot the read coverage for", | |
32 "id": 1, | |
33 "input_connections": {}, | |
34 "inputs": [ | |
35 { | |
36 "description": "BED or INTERVAL file of genome regions to plot the read coverage for", | |
37 "name": "regions" | |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
41 "outputs": [], | |
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44 "top": 239 | |
45 }, | |
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47 "tool_id": null, | |
48 "tool_state": "{\"name\": \"regions\"}", | |
49 "tool_version": null, | |
50 "type": "data_input", | |
51 "user_outputs": [] | |
52 }, | |
53 "2": { | |
54 "annotation": "sorted BAM file", | |
55 "id": 2, | |
56 "input_connections": {}, | |
57 "inputs": [ | |
58 { | |
59 "description": "sorted BAM file", | |
60 "name": "file 2 of mapped reads, e.g. control sample" | |
61 } | |
62 ], | |
63 "name": "Input dataset", | |
64 "outputs": [], | |
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67 "top": 594.5 | |
68 }, | |
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70 "tool_id": null, | |
71 "tool_state": "{\"name\": \"file 2 of mapped reads, e.g. control sample\"}", | |
72 "tool_version": null, | |
73 "type": "data_input", | |
74 "user_outputs": [] | |
75 }, | |
76 "3": { | |
77 "annotation": "generates a normalized coverage file (bigWig format)", | |
78 "id": 3, | |
79 "input_connections": { | |
80 "bamFile1": { | |
81 "id": 0, | |
82 "output_name": "output" | |
83 }, | |
84 "bamFile2": { | |
85 "id": 2, | |
86 "output_name": "output" | |
87 } | |
88 }, | |
89 "inputs": [ | |
90 { | |
91 "description": "runtime parameter for tool bamCompare", | |
92 "name": "region" | |
93 }, | |
94 { | |
95 "description": "runtime parameter for tool bamCompare", | |
96 "name": "advancedOpt" | |
97 }, | |
98 { | |
99 "description": "runtime parameter for tool bamCompare", | |
100 "name": "fragmentLength" | |
101 } | |
102 ], | |
103 "name": "bamCompare", | |
104 "outputs": [ | |
105 { | |
106 "name": "outFileName", | |
107 "type": "bigwig" | |
108 } | |
109 ], | |
110 "position": { | |
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120 "RenameDatasetActionoutFileName": { | |
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122 "newname": "BAM1_vs_BAM2_log2ratio.bigwig" | |
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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\\\"}\"}", | |
131 "tool_version": "1.0.4", | |
132 "type": "tool", | |
133 "user_outputs": [] | |
134 }, | |
135 "4": { | |
136 "annotation": "", | |
137 "id": 4, | |
138 "input_connections": { | |
139 "regionsFiles_0|regionsFile": { | |
140 "id": 1, | |
141 "output_name": "output" | |
142 }, | |
143 "scoreFile": { | |
144 "id": 3, | |
145 "output_name": "outFileName" | |
146 } | |
147 }, | |
148 "inputs": [], | |
149 "name": "computeMatrix", | |
150 "outputs": [ | |
151 { | |
152 "name": "outFileName", | |
153 "type": "bgzip" | |
154 }, | |
155 { | |
156 "name": "outFileNameData", | |
157 "type": "tabular" | |
158 }, | |
159 { | |
160 "name": "outFileSortedRegions", | |
161 "type": "bed" | |
162 }, | |
163 { | |
164 "name": "outFileNameMatrix", | |
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186 "output_name": "outFileSortedRegions" | |
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188 "RenameDatasetActionoutFileName": { | |
189 "action_arguments": { | |
190 "newname": "computeMatrix: matrix of coverage values for BED file" | |
191 }, | |
192 "action_type": "RenameDatasetAction", | |
193 "output_name": "outFileName" | |
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196 "tool_errors": null, | |
197 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.4", | |
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\\\"}}]\"}", | |
199 "tool_version": "1.0.4", | |
200 "type": "tool", | |
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202 }, | |
203 "5": { | |
204 "annotation": "create a heatmap, if wanted, kmeans clustering can be performed", | |
205 "id": 5, | |
206 "input_connections": { | |
207 "matrixFile": { | |
208 "id": 4, | |
209 "output_name": "outFileName" | |
210 } | |
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214 "description": "runtime parameter for tool heatmapper", | |
215 "name": "output" | |
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217 { | |
218 "description": "runtime parameter for tool heatmapper", | |
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221 { | |
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232 }, | |
233 { | |
234 "description": "runtime parameter for tool heatmapper", | |
235 "name": "advancedOpt" | |
236 } | |
237 ], | |
238 "name": "heatmapper", | |
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240 { | |
241 "name": "outFileName", | |
242 "type": "png" | |
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