Mercurial > repos > wolma > mimodd_workflows
comparison Galaxy-Workflow-MiModD_example_workflow_3.ga @ 1:87bfe31ce878 default tip
workflows for MiModD 0.1.6
| author | Wolfgang Maier |
|---|---|
| date | Thu, 04 Jun 2015 18:19:52 +0200 |
| parents | 9f64313f2ccb |
| children |
comparison
equal
deleted
inserted
replaced
| 0:9f64313f2ccb | 1:87bfe31ce878 |
|---|---|
| 9 "id": 0, | 9 "id": 0, |
| 10 "input_connections": {}, | 10 "input_connections": {}, |
| 11 "inputs": [ | 11 "inputs": [ |
| 12 { | 12 { |
| 13 "description": "", | 13 "description": "", |
| 14 "name": "Input Dataset" | 14 "name": "Reference Genome" |
| 15 } | 15 } |
| 16 ], | 16 ], |
| 17 "label": null, | |
| 17 "name": "Input dataset", | 18 "name": "Input dataset", |
| 18 "outputs": [], | 19 "outputs": [], |
| 19 "position": { | 20 "position": { |
| 20 "left": 172, | 21 "left": 200, |
| 21 "top": 176 | 22 "top": 391 |
| 22 }, | 23 }, |
| 23 "tool_errors": null, | 24 "tool_errors": null, |
| 24 "tool_id": null, | 25 "tool_id": null, |
| 25 "tool_state": "{\"name\": \"Input Dataset\"}", | 26 "tool_state": "{\"name\": \"Reference Genome\"}", |
| 26 "tool_version": null, | 27 "tool_version": null, |
| 27 "type": "data_input", | 28 "type": "data_input", |
| 28 "user_outputs": [] | 29 "user_outputs": [], |
| 30 "uuid": "None" | |
| 29 }, | 31 }, |
| 30 "1": { | 32 "1": { |
| 31 "annotation": "", | 33 "annotation": "", |
| 32 "id": 1, | 34 "id": 1, |
| 35 "input_connections": {}, | |
| 36 "inputs": [ | |
| 37 { | |
| 38 "description": "", | |
| 39 "name": "Hawaiian strain variants file" | |
| 40 } | |
| 41 ], | |
| 42 "label": null, | |
| 43 "name": "Input dataset", | |
| 44 "outputs": [], | |
| 45 "position": { | |
| 46 "left": 707.5, | |
| 47 "top": 335 | |
| 48 }, | |
| 49 "tool_errors": null, | |
| 50 "tool_id": null, | |
| 51 "tool_state": "{\"name\": \"Hawaiian strain variants file\"}", | |
| 52 "tool_version": null, | |
| 53 "type": "data_input", | |
| 54 "user_outputs": [], | |
| 55 "uuid": "80c25284-13aa-4172-bb52-2e8adee43626" | |
| 56 }, | |
| 57 "2": { | |
| 58 "annotation": "", | |
| 59 "id": 2, | |
| 33 "input_connections": { | 60 "input_connections": { |
| 34 "ref_genome": { | 61 "ref_genome": { |
| 35 "id": 0, | 62 "id": 0, |
| 36 "output_name": "output" | 63 "output_name": "output" |
| 37 } | 64 } |
| 38 }, | 65 }, |
| 39 "inputs": [], | 66 "inputs": [], |
| 67 "label": null, | |
| 40 "name": "SNAP Read Alignment", | 68 "name": "SNAP Read Alignment", |
| 41 "outputs": [ | 69 "outputs": [ |
| 42 { | 70 { |
| 43 "name": "outputfile", | 71 "name": "outputfile", |
| 44 "type": "bam" | 72 "type": "bam" |
| 45 } | 73 } |
| 46 ], | 74 ], |
| 47 "position": { | 75 "position": { |
| 48 "left": 359, | 76 "left": 334, |
| 49 "top": 368 | 77 "top": 607 |
| 50 }, | 78 }, |
| 51 "post_job_actions": {}, | 79 "post_job_actions": {}, |
| 52 "tool_errors": null, | 80 "tool_errors": null, |
| 53 "tool_id": "read_alignment", | 81 "tool_id": "read_alignment", |
| 54 "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"maxhits\\\": \\\"250\\\", \\\"max_mate_overlap\\\": \\\"0\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", | 82 "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 1, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"single\\\", \\\"__current_case__\\\": 0}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"discard_overlapping_mates\\\": \\\"\\\", \\\"maxhits\\\": \\\"250\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", |
| 55 "tool_version": "1.0.0", | 83 "tool_version": "1.0.0", |
| 56 "type": "tool", | 84 "type": "tool", |
| 57 "user_outputs": [] | 85 "user_outputs": [], |
| 58 }, | 86 "uuid": "None" |
| 59 "2": { | 87 }, |
| 60 "annotation": "", | 88 "3": { |
| 61 "id": 2, | 89 "annotation": "", |
| 90 "id": 3, | |
| 62 "input_connections": { | 91 "input_connections": { |
| 63 "list_input_0|inputfile": { | 92 "list_input_0|inputfile": { |
| 64 "id": 1, | 93 "id": 2, |
| 65 "output_name": "outputfile" | 94 "output_name": "outputfile" |
| 66 }, | 95 }, |
| 67 "ref_genome": { | 96 "ref_genome": { |
| 68 "id": 0, | 97 "id": 0, |
| 69 "output_name": "output" | 98 "output_name": "output" |
| 70 } | 99 } |
| 71 }, | 100 }, |
| 72 "inputs": [], | 101 "inputs": [], |
| 102 "label": null, | |
| 73 "name": "Variant Calling", | 103 "name": "Variant Calling", |
| 74 "outputs": [ | 104 "outputs": [ |
| 75 { | 105 { |
| 76 "name": "output_vcf", | 106 "name": "output_vcf", |
| 77 "type": "bcf" | 107 "type": "bcf" |
| 78 } | 108 } |
| 79 ], | 109 ], |
| 80 "position": { | 110 "position": { |
| 81 "left": 708, | 111 "left": 692, |
| 82 "top": 364 | 112 "top": 607 |
| 83 }, | 113 }, |
| 84 "post_job_actions": {}, | 114 "post_job_actions": {}, |
| 85 "tool_errors": null, | 115 "tool_errors": null, |
| 86 "tool_id": "variant_calling", | 116 "tool_id": "variant_calling", |
| 87 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", | 117 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", |
| 88 "tool_version": "1.0.0", | 118 "tool_version": "1.0.0", |
| 89 "type": "tool", | 119 "type": "tool", |
| 90 "user_outputs": [] | 120 "user_outputs": [], |
| 91 }, | 121 "uuid": "None" |
| 92 "3": { | 122 }, |
| 93 "annotation": "", | 123 "4": { |
| 94 "id": 3, | 124 "annotation": "", |
| 125 "id": 4, | |
| 95 "input_connections": { | 126 "input_connections": { |
| 96 "ifile": { | 127 "ifile": { |
| 97 "id": 2, | 128 "id": 3, |
| 98 "output_name": "output_vcf" | 129 "output_name": "output_vcf" |
| 99 } | 130 }, |
| 100 }, | 131 "sitesinfo_0|pre_vcf": { |
| 101 "inputs": [], | 132 "id": 1, |
| 133 "output_name": "output" | |
| 134 } | |
| 135 }, | |
| 136 "inputs": [], | |
| 137 "label": null, | |
| 102 "name": "Extract Variant Sites", | 138 "name": "Extract Variant Sites", |
| 103 "outputs": [ | 139 "outputs": [ |
| 104 { | 140 { |
| 105 "name": "output_vcf", | 141 "name": "output_vcf", |
| 106 "type": "vcf" | 142 "type": "vcf" |
| 107 } | 143 } |
| 108 ], | 144 ], |
| 109 "position": { | 145 "position": { |
| 110 "left": 1104.5, | 146 "left": 973.5, |
| 111 "top": 227 | 147 "top": 483 |
| 112 }, | 148 }, |
| 113 "post_job_actions": {}, | 149 "post_job_actions": {}, |
| 114 "tool_errors": null, | 150 "tool_errors": null, |
| 115 "tool_id": "extract_variants", | 151 "tool_id": "extract_variants", |
| 116 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", | 152 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[{\\\"__index__\\\": 0, \\\"pre_vcf\\\": null}]\", \"__rerun_remap_job_id__\": null}", |
| 117 "tool_version": "1.0.0", | 153 "tool_version": "1.0.0", |
| 118 "type": "tool", | 154 "type": "tool", |
| 119 "user_outputs": [] | 155 "user_outputs": [], |
| 120 }, | 156 "uuid": "None" |
| 121 "4": { | 157 }, |
| 122 "annotation": "", | 158 "5": { |
| 123 "id": 4, | 159 "annotation": "", |
| 160 "id": 5, | |
| 124 "input_connections": { | 161 "input_connections": { |
| 125 "ifile": { | 162 "ifile": { |
| 126 "id": 2, | 163 "id": 3, |
| 127 "output_name": "output_vcf" | 164 "output_name": "output_vcf" |
| 128 } | 165 } |
| 129 }, | 166 }, |
| 130 "inputs": [], | 167 "inputs": [], |
| 168 "label": null, | |
| 131 "name": "Coverage Statistics", | 169 "name": "Coverage Statistics", |
| 132 "outputs": [ | 170 "outputs": [ |
| 133 { | 171 { |
| 134 "name": "output_vcf", | 172 "name": "output_vcf", |
| 135 "type": "tabular" | 173 "type": "tabular" |
| 136 } | 174 } |
| 137 ], | 175 ], |
| 138 "position": { | 176 "position": { |
| 139 "left": 1133, | 177 "left": 1054, |
| 140 "top": 455 | 178 "top": 726 |
| 141 }, | 179 }, |
| 142 "post_job_actions": {}, | 180 "post_job_actions": {}, |
| 143 "tool_errors": null, | 181 "tool_errors": null, |
| 144 "tool_id": "coverage_stats", | 182 "tool_id": "coverage_stats", |
| 145 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", | 183 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", |
| 146 "tool_version": "1.0.0", | 184 "tool_version": "1.0.0", |
| 147 "type": "tool", | 185 "type": "tool", |
| 148 "user_outputs": [] | 186 "user_outputs": [], |
| 149 }, | 187 "uuid": "None" |
| 150 "5": { | 188 }, |
| 151 "annotation": "", | 189 "6": { |
| 152 "id": 5, | 190 "annotation": "", |
| 153 "input_connections": { | 191 "id": 6, |
| 154 "covfile": { | 192 "input_connections": { |
| 155 "id": 2, | 193 "ifile": { |
| 194 "id": 4, | |
| 156 "output_name": "output_vcf" | 195 "output_name": "output_vcf" |
| 157 }, | 196 } |
| 158 "list_input_0|bamfile": { | 197 }, |
| 159 "id": 1, | 198 "inputs": [ |
| 160 "output_name": "outputfile" | 199 { |
| 161 } | 200 "description": "runtime parameter for tool Prepare variant data for mapping", |
| 162 }, | 201 "name": "sample" |
| 163 "inputs": [], | 202 }, |
| 164 "name": "Deletion Prediction for paired-end data", | 203 { |
| 165 "outputs": [ | 204 "description": "runtime parameter for tool Prepare variant data for mapping", |
| 166 { | 205 "name": "run" |
| 167 "name": "outputfile", | 206 }, |
| 168 "type": "gff" | 207 { |
| 169 } | 208 "description": "runtime parameter for tool Prepare variant data for mapping", |
| 170 ], | 209 "name": "run" |
| 171 "position": { | 210 } |
| 172 "left": 1064, | 211 ], |
| 173 "top": 667 | 212 "label": null, |
| 174 }, | 213 "name": "Prepare variant data for mapping", |
| 175 "post_job_actions": {}, | 214 "outputs": [ |
| 176 "tool_errors": null, | 215 { |
| 177 "tool_id": "deletion_prediction", | 216 "name": "ofile", |
| 178 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", | 217 "type": "vcf" |
| 179 "tool_version": "1.0.0", | 218 }, |
| 180 "type": "tool", | 219 { |
| 181 "user_outputs": [] | 220 "name": "dictfile", |
| 221 "type": "tabular" | |
| 222 } | |
| 223 ], | |
| 224 "position": { | |
| 225 "left": 1209.5, | |
| 226 "top": 200 | |
| 227 }, | |
| 228 "post_job_actions": {}, | |
| 229 "tool_errors": null, | |
| 230 "tool_id": "cloudmap_prepare", | |
| 231 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"run\": \"{\\\"infer_missing\\\": \\\"False\\\", \\\"related_parent_sample\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"mode\\\": \\\"VAF\\\", \\\"__current_case__\\\": 1, \\\"unrelated_parent_sample\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"seqdict\": \"\\\"True\\\"\", \"sample\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | |
| 232 "tool_version": "1.0.0", | |
| 233 "type": "tool", | |
| 234 "user_outputs": [], | |
| 235 "uuid": "6225f501-6db8-4c83-ad42-59a8f1330a55" | |
| 182 } | 236 } |
| 183 } | 237 }, |
| 238 "uuid": "0a619835-3d93-489f-8d0d-93a567536404" | |
| 184 } | 239 } |
