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2 "a_galaxy_workflow": "true",
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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "MMuFLR_Human_from_MPileup_v1.4",
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6 "steps": {
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12 {
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15 }
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28 "user_outputs": []
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34 "inputs": [
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35 {
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38 }
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41 "outputs": [],
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52 },
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55 "id": 2,
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58 {
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60 "name": "VCF file of additional known variants "
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61 }
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109 },
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114 "dbSnp": {
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153 "dbSnp": {
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380 "12": {
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381 "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence",
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382 "id": 12,
|
|
|
383 "input_connections": {
|
|
|
384 "snp_effect_vcf": {
|
|
|
385 "id": 11,
|
|
|
386 "output_name": "output"
|
|
|
387 }
|
|
|
388 },
|
|
|
389 "inputs": [],
|
|
|
390 "name": "SnpEff Ensembl CDS",
|
|
|
391 "outputs": [
|
|
|
392 {
|
|
|
393 "name": "html_report",
|
|
|
394 "type": "html"
|
|
|
395 },
|
|
|
396 {
|
|
|
397 "name": "tsv_report",
|
|
|
398 "type": "tabular"
|
|
|
399 },
|
|
|
400 {
|
|
|
401 "name": "text_report",
|
|
|
402 "type": "text"
|
|
|
403 }
|
|
|
404 ],
|
|
|
405 "position": {
|
|
|
406 "left": 2497,
|
|
|
407 "top": 381
|
|
|
408 },
|
|
|
409 "post_job_actions": {
|
|
|
410 "HideDatasetActiontext_report": {
|
|
|
411 "action_arguments": {},
|
|
|
412 "action_type": "HideDatasetAction",
|
|
|
413 "output_name": "text_report"
|
|
|
414 }
|
|
|
415 },
|
|
|
416 "tool_errors": null,
|
|
|
417 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2",
|
|
|
418 "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}",
|
|
|
419 "tool_version": "1.2",
|
|
|
420 "type": "tool",
|
|
|
421 "user_outputs": []
|
|
|
422 }
|
|
|
423 }
|
|
|
424 } |
