| Previous changeset 4:6c284cb55352 (2013-04-21) Next changeset 6:2aa99b7f90f4 (2013-05-30) |
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Commit message:
Adding Galaxy-Workflow-MMuFF.ga (version 1.4 updated for SnpEff v3.2 and snpeff_cds_report v1.2) |
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added:
Galaxy-Workflow-MMuFF.ga |
| b |
| diff -r 6c284cb55352 -r 60a6f2d92058 Galaxy-Workflow-MMuFF.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MMuFF.ga Sun May 26 08:17:53 2013 -0500 |
| [ |
| b'@@ -0,0 +1,945 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "MMuFF_Human_v1.4", \n+ "steps": {\n+ "0": {\n+ "annotation": "Human RNA-seq paired reads left mates", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "Human RNA-seq paired reads left mates", \n+ "name": "Forward reads fastq"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 240, \n+ "top": 314\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Forward reads fastq\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "Human RNA-seq paired reads right mates", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "Human RNA-seq paired reads right mates", \n+ "name": "Reverse reads fastq"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 249, \n+ "top": 410\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Reverse reads fastq\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "Known SNPs - dbSNP.vcf", \n+ "id": 2, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "Known SNPs - dbSNP.vcf", \n+ "name": "VCF file of known variants (dbSNP)"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 2362, \n+ "top": 745\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"VCF file of known variants (dbSNP)\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "3": {\n+ "annotation": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \\nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)", \n+ "id": 3, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \\nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)", \n+ "name": "VCF file of additional known variants "\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 4388, \n+ "top": 576\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"VCF file of additional known variants \\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "4": {\n+ "annotation": "Convert quality scores to sanger scale", \n+ "id": 4, \n+ "input_connections": {\n+ "input_file": {\n+ "id": 0, \n+ '..b't": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "text_report"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", \n+ "tool_state": "{\\"ensembl_host\\": \\"\\\\\\"feb2012\\\\\\"\\", \\"report_format\\": \\"[\\\\\\"html\\\\\\", \\\\\\"tsv\\\\\\"]\\", \\"ensembl_dataset\\": \\"\\\\\\"hsapiens_gene_ensembl\\\\\\"\\", \\"__page__\\": 0, \\"effects_filter\\": \\"\\\\\\"FRAME_SHIFT\\\\\\"\\", \\"polya\\": \\"\\\\\\"5\\\\\\"\\", \\"all_effects\\": \\"\\\\\\"False\\\\\\"\\", \\"snpeff_aa_change\\": \\"\\\\\\"False\\\\\\"\\", \\"snp_effect_vcf\\": \\"null\\", \\"with_ccds\\": \\"\\\\\\"False\\\\\\"\\"}", \n+ "tool_version": "1.2", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "25": {\n+ "annotation": "Ignore variations in SPLICE donor/acceptor regions", \n+ "id": 25, \n+ "input_connections": {\n+ "input": {\n+ "id": 23, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "SnpSift Filter", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "vcf"\n+ }\n+ ], \n+ "position": {\n+ "left": 5851, \n+ "top": 532\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2", \n+ "tool_state": "{\\"__page__\\": 0, \\"inverse\\": \\"\\\\\\"True\\\\\\"\\", \\"addFilter\\": \\"\\\\\\"\\\\\\"\\", \\"rmFilter\\": \\"\\\\\\"\\\\\\"\\", \\"expr\\": \\"\\\\\\"( EFF[ANY].EFFECT =~ \'SPLICE\' )\\\\\\"\\", \\"filterId\\": \\"\\\\\\"\\\\\\"\\", \\"pass\\": \\"\\\\\\"False\\\\\\"\\", \\"input\\": \\"null\\"}", \n+ "tool_version": "3.2", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "26": {\n+ "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", \n+ "id": 26, \n+ "input_connections": {\n+ "snp_effect_vcf": {\n+ "id": 25, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "SnpEff Ensembl CDS", \n+ "outputs": [\n+ {\n+ "name": "html_report", \n+ "type": "html"\n+ }, \n+ {\n+ "name": "tsv_report", \n+ "type": "tabular"\n+ }, \n+ {\n+ "name": "text_report", \n+ "type": "text"\n+ }\n+ ], \n+ "position": {\n+ "left": 6067, \n+ "top": 502\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActiontext_report": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "text_report"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2", \n+ "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\\\\\\"\\"}", \n+ "tool_version": "1.2", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |