| Previous changeset 1:95efdc025a48 (2015-11-12) Next changeset 3:025efd59ddd0 (2015-11-18) |
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Commit message:
Uploaded |
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modified:
Galaxy-Workflow-workflow_gandalf_3.0.ga repository_dependencies.xml |
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added:
Galaxy-Workflow-creation_workflow_gandalf_2.0.ga |
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removed:
Galaxy-Workflow-workflow_gandalf_1.0.ga |
| b |
| diff -r 95efdc025a48 -r cfc5177134ce Galaxy-Workflow-creation_workflow_gandalf_2.0.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Wed Nov 18 09:14:53 2015 -0500 |
| [ |
| b'@@ -0,0 +1,384 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "creation workflow gandalf 2.0", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 288, \n+ "top": 200\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 288, \n+ "top": 285\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ 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| b |
| diff -r 95efdc025a48 -r cfc5177134ce Galaxy-Workflow-workflow_gandalf_1.0.ga --- a/Galaxy-Workflow-workflow_gandalf_1.0.ga Thu Nov 12 07:40:16 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,320 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "workflow gandalf 1.0", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 467, \n- "top": 200\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "1": {\n- "annotation": "", \n- "id": 1, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 467, \n- "top": 320\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n- "tool_version": null, \n- "type": 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"name": "VCFFiltering", \n- "outputs": [\n- {\n- "name": "outputVCF", \n- "type": "vcf"\n- }, \n- {\n- "name": "output_html", \n- "type": "html"\n- }\n- ], \n- "position": {\n- "left": 1714, \n- "top": 180\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionoutputVCF": {\n- "action_arguments": {\n- "newname": "#{inputVCF | basename}.filteredVCF"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "outputVCF"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "10.0.0.125:9009/repos/urgiteam/vcfgandalftools/VCFFiltering/0.01", \n- "tool_state": "{\\"inputVCF\\": \\"null\\", \\"BedFile_List\\": \\"{\\\\\\"is_BedFile\\\\\\": \\\\\\"False\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"AF\\": \\"\\\\\\"0.9\\\\\\"\\", \\"__page__\\": 0, \\"DP_auto\\": \\"{\\\\\\"is_DP_auto\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"__rerun_remap_job_id__\\": null, \\"AN\\": \\"\\\\\\"2\\\\\\"\\", \\"chromInfo\\": 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| b |
| diff -r 95efdc025a48 -r cfc5177134ce Galaxy-Workflow-workflow_gandalf_3.0.ga --- a/Galaxy-Workflow-workflow_gandalf_3.0.ga Thu Nov 12 07:40:16 2015 -0500 +++ b/Galaxy-Workflow-workflow_gandalf_3.0.ga Wed Nov 18 09:14:53 2015 -0500 |
| [ |
| b'@@ -18,7 +18,7 @@\n "outputs": [], \n "position": {\n "left": 258, \n- "top": 260\n+ "top": 593\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -41,7 +41,7 @@\n "outputs": [], \n "position": {\n "left": 258, \n- "top": 352\n+ "top": 685\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -64,7 +64,7 @@\n "outputs": [], \n "position": {\n "left": 252, \n- "top": 440\n+ "top": 773\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -87,7 +87,7 @@\n "outputs": [], \n "position": {\n "left": 241, \n- "top": 520\n+ "top": 853\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -110,7 +110,7 @@\n "outputs": [], \n "position": {\n "left": 245, \n- "top": 605\n+ "top": 938\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -123,6 +123,56 @@\n "annotation": "", \n "id": 5, \n "input_connections": {\n+ "fastq_input|fastq_input1": {\n+ "id": 2, \n+ "output_name": "output"\n+ }, \n+ "fastq_input|fastq_input2": {\n+ "id": 0, \n+ "output_name": "output"\n+ }, \n+ "reference_source|ref_file": {\n+ "id": 4, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Map with BWA-MEM", \n+ "outputs": [\n+ {\n+ "name": "bam_output", \n+ "type": "bam"\n+ }\n+ ], \n+ "position": {\n+ "left": 527, \n+ "top": 929\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionbam_output": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "bam_output"\n+ }, \n+ "RenameDatasetActionbam_output": {\n+ "action_arguments": {\n+ "newname": "#{fastq_input1 | basename}.bam"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "bam_output"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", \n+ "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"__workflow_invocation_uuid__\\": \\"\\\\\\"519bd5da87bc11e5aa509e87638b9e35\\\\\\"\\", \\"rg\\": \\"{\\\\\\"rg_selector\\\\\\": \\\\\\"set_picard\\\\\\", 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\\"analysis_type\\": \\"{\\\\\\"analysis_type_selector\\\\\\": \\\\\\"full\\\\\\", \\\\\\"algorithmic_options\\\\\\": {\\\\\\"algorithmic_options_selector\\\\\\": \\\\\\"do_not_set\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"io_options'..b'20 @@\n "tool_errors": null, \n "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", \n "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__workflow_invocation_uuid__\\": \\"\\\\\\"6333a3ae87bc11e591529e87638b9e35\\\\\\"\\"}", \n- "tool_version": "1.0.0", \n+ "tool_version": "1.0.1", \n "type": "tool", \n "user_outputs": []\n }, \n- "17": {\n+ "16": {\n "annotation": "", \n- "id": 17, \n+ "id": 16, \n "input_connections": {\n "BedFile_List|BedFiles_0|inputBed": {\n "id": 6, \n "output_name": "output_bed"\n }, \n "inputVCF": {\n- "id": 13, \n+ "id": 12, \n "output_name": "output_vcf_firstBAM"\n }\n }, \n@@ -786,7 +726,7 @@\n ], \n "position": {\n "left": 1739, \n- "top": 260\n+ "top": 593\n }, \n "post_job_actions": {\n "HideDatasetActionoutputVCF": {\n@@ -821,16 +761,16 @@\n "type": "tool", \n "user_outputs": []\n }, \n- "18": {\n+ "17": {\n "annotation": "", \n- "id": 18, \n+ "id": 17, \n "input_connections": {\n "BedFile_List|BedFiles_0|inputBed": {\n- "id": 5, \n+ "id": 6, \n "output_name": "output_bed"\n }, \n "inputVCF": {\n- "id": 15, \n+ "id": 14, \n "output_name": "output_vcf_firstBAM"\n }\n }, \n@@ -848,7 +788,7 @@\n ], \n "position": {\n "left": 1739, \n- "top": 445\n+ "top": 778\n }, \n "post_job_actions": {\n "HideDatasetActionoutputVCF": {\n@@ -883,16 +823,16 @@\n "type": "tool", \n "user_outputs": []\n }, \n- "19": {\n+ "18": {\n "annotation": "", \n- "id": 19, \n+ "id": 18, \n "input_connections": {\n "VCFFile_0|inputStrainVCF": {\n- "id": 17, \n+ "id": 16, \n "output_name": "outputVCF"\n }, \n "VCFFile_1|inputStrainVCF": {\n- "id": 18, \n+ "id": 17, \n "output_name": "outputVCF"\n }, \n "inputFasta": {\n@@ -910,7 +850,7 @@\n ], \n "position": {\n "left": 2067, \n- "top": 260\n+ "top": 593\n }, \n "post_job_actions": {\n "HideDatasetActionoutputVCFStorage": {\n@@ -933,12 +873,12 @@\n "type": "tool", \n "user_outputs": []\n }, \n- "20": {\n+ "19": {\n "annotation": "", \n- "id": 20, \n+ "id": 19, \n "input_connections": {\n "inputTabular": {\n- "id": 19, \n+ "id": 18, \n "output_name": "outputVCFStorage"\n }\n }, \n@@ -960,7 +900,7 @@\n ], \n "position": {\n "left": 2387, \n- "top": 260\n+ "top": 593\n }, \n "post_job_actions": {\n "HideDatasetActionoutput_bed": {\n@@ -989,5 +929,5 @@\n "user_outputs": []\n }\n }, \n- "uuid": "7924e8b4-f601-4a2e-a768-203f86c4f94e"\n+ "uuid": "359c9c1b-1771-475c-b353-1b9a0d802f18"\n }\n\\ No newline at end of file\n' |
| b |
| diff -r 95efdc025a48 -r cfc5177134ce repository_dependencies.xml --- a/repository_dependencies.xml Thu Nov 12 07:40:16 2015 -0500 +++ b/repository_dependencies.xml Wed Nov 18 09:14:53 2015 -0500 |
| b |
| @@ -6,4 +6,5 @@ <repository changeset_revision="874dd6c0fcde" name="freebayes4workflow" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="3552a8d9f51c" name="vcfgandalftools" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="af65bfb54977" name="suite_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="cc6db1ee2d48" name="mdust" owner=" urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories> |