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Commit message:
Uploaded the workflow |
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added:
Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga |
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| diff -r 000000000000 -r 39ec6ecd0e3b Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga Thu Oct 27 09:19:13 2011 -0400 |
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| b'@@ -0,0 +1,1246 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "mt analysis 0.01 strand-specific (fastq double)", \n+ "steps": {\n+ "0": {\n+ "annotation": "The second input dataset. Usually the second PCR replicate for a given sample.", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "name": "Map with BWA", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "sam"\n+ }\n+ ], \n+ "position": {\n+ "left": 229, \n+ "top": 388\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "bwa_wrapper", \n+ "tool_state": "{\\"genomeSource\\": \\"{\\\\\\"indices\\\\\\": \\\\\\"/mnt/galaxyIndices/hg19/bwa/base/hg19\\\\\\", \\\\\\"refGenomeSource\\\\\\": \\\\\\"indexed\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"paired\\": \\"{\\\\\\"sPaired\\\\\\": \\\\\\"single\\\\\\", \\\\\\"input1\\\\\\": null, \\\\\\"__current_case__\\\\\\": 0}\\", \\"params\\": \\"{\\\\\\"__current_case__\\\\\\": 0, \\\\\\"source_select\\\\\\": \\\\\\"pre_set\\\\\\"}\\", \\"suppressHeader\\": \\"\\\\\\"True\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.0.3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "The first input dataset. Usually the first PCR replicate for a given sample.", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "name": "Map with BWA", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "sam"\n+ }\n+ ], \n+ "position": {\n+ "left": 229, \n+ "top": 154\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "bwa_wrapper", \n+ "tool_state": "{\\"genomeSource\\": \\"{\\\\\\"indices\\\\\\": \\\\\\"/mnt/galaxyIndices/hg19/bwa/base/hg19\\\\\\", \\\\\\"refGenomeSource\\\\\\": \\\\\\"indexed\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"paired\\": \\"{\\\\\\"sPaired\\\\\\": \\\\\\"single\\\\\\", \\\\\\"input1\\\\\\": null, \\\\\\"__current_case__\\\\\\": 0}\\", \\"params\\": \\"{\\\\\\"__current_case__\\\\\\": 0, \\\\\\"source_select\\\\\\": \\\\\\"pre_set\\\\\\"}\\", \\"suppressHeader\\": \\"\\\\\\"True\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.0.3", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "Here SAM datasets generated by BWA are merged together", \n+ "id": 2, \n+ "input_connections": {\n+ "input1": {\n+ "id": 1, \n+ "output_name": "output"\n+ }, \n+ "queries_0|input2": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Concatenate queries", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 410, \n+ "top": 257\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "cat1", \n+ "tool_state": "{\\"__page__\\": 0, \\"input1\\": \\"null\\", \\"queries\\": \\"[{\\\\\\"input2\\\\\\": null, \\\\\\"__index__\\\\\\": 0}]\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "3": {\n+ "annotation": "By selecting only lines containing the X0:i:1 tag we eliminate reads that map multiple times. Thus this step removes reads that map more than once.", \n+ "id": 3, \n+ "input_connections": {\n+ "input": {\n+ "id": 2, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "na'..b'": {\n+ "id": 38, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Compute", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 2221, \n+ "top": 831\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Add_a_column1", \n+ "tool_state": "{\\"input\\": \\"null\\", \\"cond\\": \\"\\\\\\"c7+c18\\\\\\"\\", \\"round\\": \\"\\\\\\"yes\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.1.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "40": {\n+ "annotation": "... summing up all Ts (column 8 in PLUS and column 19 in MINUS)", \n+ "id": 40, \n+ "input_connections": {\n+ "input": {\n+ "id": 39, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Compute", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 2289, \n+ "top": 716\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Add_a_column1", \n+ "tool_state": "{\\"input\\": \\"null\\", \\"cond\\": \\"\\\\\\"c8+c19\\\\\\"\\", \\"round\\": \\"\\\\\\"yes\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.1.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "41": {\n+ "annotation": "... summing up coverage (column 9 in PLUS and column 20 in MINUS)", \n+ "id": 41, \n+ "input_connections": {\n+ "input": {\n+ "id": 40, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Compute", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 2344, \n+ "top": 598\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Add_a_column1", \n+ "tool_state": "{\\"input\\": \\"null\\", \\"cond\\": \\"\\\\\\"c9+c20\\\\\\"\\", \\"round\\": \\"\\\\\\"yes\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.1.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "42": {\n+ "annotation": "Finally, we clean up all unnecessary columns and generate a combined dataset that will contain 10 columns:\\n[1] Chromosome\\n[2] Start\\n[3] End\\n[4] Base in the reference genome\\n[5] Number of As\\n[6] Number of Cs\\n[7] Number of Gs\\n[8] Number of Ts\\n[9] Coverage at that position\\n[10] Number of variants (differences from reference abve 1% level).", \n+ "id": 42, \n+ "input_connections": {\n+ "input": {\n+ "id": 41, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Cut", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 2439, \n+ "top": 1185\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Cut1", \n+ "tool_state": "{\\"columnList\\": \\"\\\\\\"c1,c2,c3,c4,c25,c26,c27,c28,c29,c24\\\\\\"\\", \\"input\\": \\"null\\", \\"delimiter\\": \\"\\\\\\"T\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.0.1", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |