Mercurial > repos > jjohnson > mmuff
changeset 4:6c284cb55352
Update SnpEff-cds-report to version 1.1
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Sun, 21 Apr 2013 16:52:18 -0500 |
| parents | 0b3a14a7b5f1 |
| children | 60a6f2d92058 |
| files | Galaxy-Workflow-MMuFF_v1.2.ga |
| diffstat | 1 files changed, 33 insertions(+), 43 deletions(-) [+] |
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--- a/Galaxy-Workflow-MMuFF_v1.2.ga Fri Apr 12 09:30:08 2013 -0500 +++ b/Galaxy-Workflow-MMuFF_v1.2.ga Sun Apr 21 16:52:18 2013 -0500 @@ -18,7 +18,7 @@ "outputs": [], "position": { "left": 240, - "top": 287 + "top": 314 }, "tool_errors": null, "tool_id": null, @@ -41,7 +41,7 @@ "outputs": [], "position": { "left": 249, - "top": 383 + "top": 410 }, "tool_errors": null, "tool_id": null, @@ -64,7 +64,7 @@ "outputs": [], "position": { "left": 2327, - "top": 758 + "top": 785 }, "tool_errors": null, "tool_id": null, @@ -87,7 +87,7 @@ "outputs": [], "position": { "left": 4388, - "top": 549 + "top": 576 }, "tool_errors": null, "tool_id": null, @@ -120,7 +120,7 @@ ], "position": { "left": 510, - "top": 264 + "top": 291 }, "post_job_actions": {}, "tool_errors": null, @@ -154,7 +154,7 @@ ], "position": { "left": 505, - "top": 404 + "top": 431 }, "post_job_actions": {}, "tool_errors": null, @@ -199,7 +199,7 @@ ], "position": { "left": 884, - "top": 305 + "top": 332 }, "post_job_actions": { "HideDatasetActiondeletions": { @@ -226,7 +226,7 @@ "user_outputs": [] }, "7": { - "annotation": "Keep only mappings with MAPQ of 255", + "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)", "id": 7, "input_connections": { "input1": { @@ -244,7 +244,7 @@ ], "position": { "left": 1154, - "top": 339 + "top": 366 }, "post_job_actions": { "HideDatasetActionoutput1": { @@ -279,7 +279,7 @@ ], "position": { "left": 1505, - "top": 296 + "top": 323 }, "post_job_actions": {}, "tool_errors": null, @@ -308,7 +308,7 @@ ], "position": { "left": 1506, - "top": 476 + "top": 503 }, "post_job_actions": {}, "tool_errors": null, @@ -337,7 +337,7 @@ ], "position": { "left": 1841, - "top": 348 + "top": 375 }, "post_job_actions": { "HideDatasetActionout_file": { @@ -376,7 +376,7 @@ ], "position": { "left": 2086, - "top": 333 + "top": 360 }, "post_job_actions": {}, "tool_errors": null, @@ -405,7 +405,7 @@ ], "position": { "left": 2401, - "top": 305 + "top": 332 }, "post_job_actions": {}, "tool_errors": null, @@ -442,7 +442,7 @@ ], "position": { "left": 2565, - "top": 491 + "top": 518 }, "post_job_actions": { "HideDatasetActionoutput_log": { @@ -485,7 +485,7 @@ ], "position": { "left": 2811, - "top": 324 + "top": 351 }, "post_job_actions": { "HideDatasetActionoutput_log": { @@ -524,7 +524,7 @@ ], "position": { "left": 3174, - "top": 291 + "top": 318 }, "post_job_actions": { "HideDatasetActionhtml_file": { @@ -568,7 +568,7 @@ ], "position": { "left": 3554, - "top": 265 + "top": 292 }, "post_job_actions": { "HideDatasetActionoutput_log": { @@ -613,7 +613,7 @@ ], "position": { "left": 4029, - "top": 296 + "top": 323 }, "post_job_actions": {}, "tool_errors": null, @@ -646,7 +646,7 @@ ], "position": { "left": 4421, - "top": 285 + "top": 312 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -685,7 +685,7 @@ ], "position": { "left": 4724, - "top": 433 + "top": 460 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -720,7 +720,7 @@ ], "position": { "left": 5043, - "top": 483 + "top": 510 }, "post_job_actions": {}, "tool_errors": null, @@ -753,7 +753,7 @@ ], "position": { "left": 5277, - "top": 442 + "top": 469 }, "post_job_actions": { "HideDatasetActionstatsFile": { @@ -788,7 +788,7 @@ ], "position": { "left": 5595, - "top": 405 + "top": 432 }, "post_job_actions": {}, "tool_errors": null, @@ -817,7 +817,7 @@ ], "position": { "left": 5600, - "top": 584 + "top": 611 }, "post_job_actions": {}, "tool_errors": null, @@ -853,8 +853,8 @@ } ], "position": { - "left": 5810, - "top": 364 + "left": 5828, + "top": 407 }, "post_job_actions": { "HideDatasetActionhtml_report": { @@ -874,9 +874,9 @@ } }, "tool_errors": null, - "tool_id": "SnpEff-cds-report", + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", - "tool_version": "1.0", + "tool_version": "1.1", "type": "tool", "user_outputs": [] }, @@ -906,30 +906,20 @@ } ], "position": { - "left": 5820, - "top": 537 + "left": 5832, + "top": 566 }, "post_job_actions": { - "HideDatasetActionhtml_report": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "html_report" - }, "HideDatasetActiontext_report": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "text_report" - }, - "HideDatasetActiontsv_report": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "tsv_report" } }, "tool_errors": null, - "tool_id": "SnpEff-cds-report", + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", - "tool_version": "1.0", + "tool_version": "1.1", "type": "tool", "user_outputs": [] }