Mercurial > repos > rnateam > blockclust_workflow
comparison blockclust_workflow.ga @ 2:e9b2400cc569 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 22 Oct 2013 17:35:13 -0400 |
| parents | |
| children | adcc8f1b6920 |
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| 1:d0ae001db6d7 | 2:e9b2400cc569 |
|---|---|
| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "", | |
| 4 "format-version": "0.1", | |
| 5 "name": "BlockClustWorkflow", | |
| 6 "steps": { | |
| 7 "0": { | |
| 8 "annotation": "", | |
| 9 "id": 0, | |
| 10 "input_connections": {}, | |
| 11 "inputs": [], | |
| 12 "name": "BlockClust", | |
| 13 "outputs": [ | |
| 14 { | |
| 15 "name": "tags_bed", | |
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| 17 }, | |
| 18 { | |
| 19 "name": "hclust_plot", | |
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| 22 { | |
| 23 "name": "clusters", | |
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| 25 }, | |
| 26 { | |
| 27 "name": "sim_tab_out", | |
| 28 "type": "tabular" | |
| 29 }, | |
| 30 { | |
| 31 "name": "analysis", | |
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| 33 }, | |
| 34 { | |
| 35 "name": "cluster_dist", | |
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| 41 "top": 308 | |
| 42 }, | |
| 43 "post_job_actions": {}, | |
| 44 "tool_errors": null, | |
| 45 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/0.1", | |
| 46 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\"}", | |
| 47 "tool_version": "0.1", | |
| 48 "type": "tool", | |
| 49 "user_outputs": [] | |
| 50 }, | |
| 51 "1": { | |
| 52 "annotation": "", | |
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| 54 "input_connections": { | |
| 55 "input": { | |
| 56 "id": 0, | |
| 57 "output_name": "tags_bed" | |
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| 59 }, | |
| 60 "inputs": [], | |
| 61 "name": "Sort", | |
| 62 "outputs": [ | |
| 63 { | |
| 64 "name": "out_file1", | |
| 65 "type": "input" | |
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| 67 ], | |
| 68 "position": { | |
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| 71 }, | |
| 72 "post_job_actions": {}, | |
| 73 "tool_errors": null, | |
| 74 "tool_id": "sort1", | |
| 75 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", | |
| 76 "tool_version": "1.0.3", | |
| 77 "type": "tool", | |
| 78 "user_outputs": [] | |
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| 80 "2": { | |
| 81 "annotation": "", | |
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| 83 "input_connections": { | |
| 84 "input": { | |
| 85 "id": 1, | |
| 86 "output_name": "out_file1" | |
| 87 } | |
| 88 }, | |
| 89 "inputs": [], | |
| 90 "name": "blockbuster", | |
| 91 "outputs": [ | |
| 92 { | |
| 93 "name": "output", | |
| 94 "type": "tabular" | |
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| 96 ], | |
| 97 "position": { | |
| 98 "left": 694, | |
| 99 "top": 308 | |
| 100 }, | |
| 101 "post_job_actions": {}, | |
| 102 "tool_errors": null, | |
| 103 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", | |
| 104 "tool_state": "{\"distance\": \"\\\"30\\\"\", \"scale\": \"\\\"0.4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"1\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"2.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"10.0\\\"\"}", | |
| 105 "tool_version": "0.1", | |
| 106 "type": "tool", | |
| 107 "user_outputs": [] | |
| 108 }, | |
| 109 "3": { | |
| 110 "annotation": "", | |
| 111 "id": 3, | |
| 112 "input_connections": { | |
| 113 "mode|input_bbo": { | |
| 114 "id": 2, | |
| 115 "output_name": "output" | |
| 116 } | |
| 117 }, | |
| 118 "inputs": [ | |
| 119 { | |
| 120 "description": "runtime parameter for tool BlockClust", | |
| 121 "name": "mode" | |
| 122 } | |
| 123 ], | |
| 124 "name": "BlockClust", | |
| 125 "outputs": [ | |
| 126 { | |
| 127 "name": "tags_bed", | |
| 128 "type": "bed" | |
| 129 }, | |
| 130 { | |
| 131 "name": "hclust_plot", | |
| 132 "type": "pdf" | |
| 133 }, | |
| 134 { | |
| 135 "name": "clusters", | |
| 136 "type": "bed" | |
| 137 }, | |
| 138 { | |
| 139 "name": "sim_tab_out", | |
| 140 "type": "tabular" | |
| 141 }, | |
| 142 { | |
| 143 "name": "analysis", | |
| 144 "type": "tabular" | |
| 145 }, | |
| 146 { | |
| 147 "name": "cluster_dist", | |
| 148 "type": "pdf" | |
| 149 } | |
| 150 ], | |
| 151 "position": { | |
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| 154 }, | |
| 155 "post_job_actions": {}, | |
| 156 "tool_errors": null, | |
| 157 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/0.1", | |
| 158 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\"}", | |
| 159 "tool_version": "0.1", | |
| 160 "type": "tool", | |
| 161 "user_outputs": [] | |
| 162 }, | |
| 163 "4": { | |
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| 166 "input_connections": { | |
| 167 "input": { | |
| 168 "id": 3, | |
| 169 "output_name": "clusters" | |
| 170 } | |
| 171 }, | |
| 172 "inputs": [], | |
| 173 "name": "Extract Genomic DNA", | |
| 174 "outputs": [ | |
| 175 { | |
| 176 "name": "out_file1", | |
| 177 "type": "input" | |
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| 179 ], | |
| 180 "position": { | |
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| 183 }, | |
| 184 "post_job_actions": {}, | |
| 185 "tool_errors": null, | |
| 186 "tool_id": "Extract genomic DNA 1", | |
| 187 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", | |
| 188 "tool_version": "2.2.2", | |
| 189 "type": "tool", | |
| 190 "user_outputs": [] | |
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| 192 "5": { | |
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| 195 "input_connections": { | |
| 196 "seqdb": { | |
| 197 "id": 4, | |
| 198 "output_name": "out_file1" | |
| 199 } | |
| 200 }, | |
| 201 "inputs": [], | |
| 202 "name": "Search covariance model(s)", | |
| 203 "outputs": [ | |
| 204 { | |
| 205 "name": "outfile", | |
| 206 "type": "tabular" | |
| 207 }, | |
| 208 { | |
| 209 "name": "multiple_alignment_output", | |
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| 219 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.1", | |
| 220 "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": null, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", | |
| 221 "tool_version": "1.1.0.1", | |
| 222 "type": "tool", | |
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| 225 "6": { | |
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| 237 "mode|sim_tab_in": { | |
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| 239 "output_name": "sim_tab_out" | |
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| 242 "inputs": [], | |
| 243 "name": "BlockClust", | |
| 244 "outputs": [ | |
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| 254 "name": "clusters", | |
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| 262 "name": "analysis", | |
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| 274 "post_job_actions": {}, | |
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| 276 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/0.1", | |
| 277 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\"}", | |
| 278 "tool_version": "0.1", | |
| 279 "type": "tool", | |
| 280 "user_outputs": [] | |
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| 282 } | |
| 283 } |
