| Previous changeset 3:0b3a14a7b5f1 (2013-04-12) Next changeset 5:60a6f2d92058 (2013-05-26) |
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Commit message:
Update SnpEff-cds-report to version 1.1 |
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modified:
Galaxy-Workflow-MMuFF_v1.2.ga |
| b |
| diff -r 0b3a14a7b5f1 -r 6c284cb55352 Galaxy-Workflow-MMuFF_v1.2.ga --- 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 |
| [ |
| b'@@ -18,7 +18,7 @@\n "outputs": [], \n "position": {\n "left": 240, \n- "top": 287\n+ "top": 314\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -41,7 +41,7 @@\n "outputs": [], \n "position": {\n "left": 249, \n- "top": 383\n+ "top": 410\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -64,7 +64,7 @@\n "outputs": [], \n "position": {\n "left": 2327, \n- "top": 758\n+ "top": 785\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -87,7 +87,7 @@\n "outputs": [], \n "position": {\n "left": 4388, \n- "top": 549\n+ "top": 576\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -120,7 +120,7 @@\n ], \n "position": {\n "left": 510, \n- "top": 264\n+ "top": 291\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -154,7 +154,7 @@\n ], \n "position": {\n "left": 505, \n- "top": 404\n+ "top": 431\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -199,7 +199,7 @@\n ], \n "position": {\n "left": 884, \n- "top": 305\n+ "top": 332\n }, \n "post_job_actions": {\n "HideDatasetActiondeletions": {\n@@ -226,7 +226,7 @@\n "user_outputs": []\n }, \n "7": {\n- "annotation": "Keep only mappings with MAPQ of 255", \n+ "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)", \n "id": 7, \n "input_connections": {\n "input1": {\n@@ -244,7 +244,7 @@\n ], \n "position": {\n "left": 1154, \n- "top": 339\n+ "top": 366\n }, \n "post_job_actions": {\n "HideDatasetActionoutput1": {\n@@ -279,7 +279,7 @@\n ], \n "position": {\n "left": 1505, \n- "top": 296\n+ "top": 323\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -308,7 +308,7 @@\n ], \n "position": {\n "left": 1506, \n- "top": 476\n+ "top": 503\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -337,7 +337,7 @@\n ], \n "position": {\n "left": 1841, \n- "top": 348\n+ "top": 375\n }, \n "post_job_actions": {\n "HideDatasetActionout_file": {\n@@ -376,7 +376,7 @@\n ], \n "position": {\n "left": 2086, \n- "top": 333\n+ "top": 360\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -405,7 +405,7 @@\n ], \n "position": {\n "left": 2401, \n- "top": 305\n+ "top": 332\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -442,7 +442,7 @@\n ], \n "position": {\n "left": 2565, \n- "top": 491\n+ "top": 518\n }, \n "post_job_actions": {\n "HideDatasetActionoutput_log": {\n@@ -485,7 +485,7 @@\n ], \n "position": {\n "left": 2811, \n- "top": 324\n+ "top": 351\n }'..b' "HideDatasetActionoutput": {\n@@ -685,7 +685,7 @@\n ], \n "position": {\n "left": 4724, \n- "top": 433\n+ "top": 460\n }, \n "post_job_actions": {\n "HideDatasetActionoutput": {\n@@ -720,7 +720,7 @@\n ], \n "position": {\n "left": 5043, \n- "top": 483\n+ "top": 510\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -753,7 +753,7 @@\n ], \n "position": {\n "left": 5277, \n- "top": 442\n+ "top": 469\n }, \n "post_job_actions": {\n "HideDatasetActionstatsFile": {\n@@ -788,7 +788,7 @@\n ], \n "position": {\n "left": 5595, \n- "top": 405\n+ "top": 432\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -817,7 +817,7 @@\n ], \n "position": {\n "left": 5600, \n- "top": 584\n+ "top": 611\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -853,8 +853,8 @@\n }\n ], \n "position": {\n- "left": 5810, \n- "top": 364\n+ "left": 5828, \n+ "top": 407\n }, \n "post_job_actions": {\n "HideDatasetActionhtml_report": {\n@@ -874,9 +874,9 @@\n }\n }, \n "tool_errors": null, \n- "tool_id": "SnpEff-cds-report", \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", \n "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\\\\\\"\\"}", \n- "tool_version": "1.0", \n+ "tool_version": "1.1", \n "type": "tool", \n "user_outputs": []\n }, \n@@ -906,30 +906,20 @@\n }\n ], \n "position": {\n- "left": 5820, \n- "top": 537\n+ "left": 5832, \n+ "top": 566\n }, \n "post_job_actions": {\n- "HideDatasetActionhtml_report": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "html_report"\n- }, \n "HideDatasetActiontext_report": {\n "action_arguments": {}, \n "action_type": "HideDatasetAction", \n "output_name": "text_report"\n- }, \n- "HideDatasetActiontsv_report": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "tsv_report"\n }\n }, \n "tool_errors": null, \n- "tool_id": "SnpEff-cds-report", \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.0", \n "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\\\\\\"\\"}", \n- "tool_version": "1.0", \n+ "tool_version": "1.1", \n "type": "tool", \n "user_outputs": []\n }\n' |