| Next changeset 1:87bfe31ce878 (2015-06-04) |
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Commit message:
Uploaded |
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added:
Galaxy-Workflow-MiModD_example_workflow_1.ga Galaxy-Workflow-MiModD_example_workflow_2.ga Galaxy-Workflow-MiModD_example_workflow_3.ga repository_dependencies.xml |
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| diff -r 000000000000 -r 9f64313f2ccb Galaxy-Workflow-MiModD_example_workflow_1.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MiModD_example_workflow_1.ga Wed Feb 11 10:06:13 2015 -0500 |
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| @@ -0,0 +1,184 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "MiModD example workflow 1", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 172, + "top": 176 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "ref_genome": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "SNAP Read Alignment", + "outputs": [ + { + "name": "outputfile", + "type": "bam" + } + ], + "position": { + "left": 359, + "top": 368 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "read_alignment", + "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"maxhits\\\": \\\"250\\\", \\\"max_mate_overlap\\\": \\\"0\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "list_input_0|inputfile": { + "id": 1, + "output_name": "outputfile" + }, + "ref_genome": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Variant Calling", + "outputs": [ + { + "name": "output_vcf", + "type": "bcf" + } + ], + "position": { + "left": 708, + "top": 364 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "variant_calling", + "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "ifile": { + "id": 2, + "output_name": "output_vcf" + } + }, + "inputs": [], + "name": "Extract Variant Sites", + "outputs": [ + { + "name": "output_vcf", + "type": "vcf" + } + ], + "position": { + "left": 1104.5, + "top": 227 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "extract_variants", + "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "ifile": { + "id": 2, + "output_name": "output_vcf" + } + }, + "inputs": [], + "name": "Coverage Statistics", + "outputs": [ + { + "name": "output_vcf", + "type": "tabular" + } + ], + "position": { + "left": 1133, + "top": 455 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "coverage_stats", + "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "covfile": { + "id": 2, + "output_name": "output_vcf" + }, + "list_input_0|bamfile": { + "id": 1, + "output_name": "outputfile" + } + }, + "inputs": [], + "name": "Deletion Prediction for paired-end data", + "outputs": [ + { + "name": "outputfile", + "type": "gff" + } + ], + "position": { + "left": 1064, + "top": 667 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "deletion_prediction", + "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file |
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| diff -r 000000000000 -r 9f64313f2ccb Galaxy-Workflow-MiModD_example_workflow_2.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MiModD_example_workflow_2.ga Wed Feb 11 10:06:13 2015 -0500 |
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| @@ -0,0 +1,184 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "MiModD example workflow 3", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 172, + "top": 174 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "ref_genome": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "SNAP Read Alignment", + "outputs": [ + { + "name": "outputfile", + "type": "bam" + } + ], + "position": { + "left": 359, + "top": 366 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "read_alignment", + "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 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| diff -r 000000000000 -r 9f64313f2ccb Galaxy-Workflow-MiModD_example_workflow_3.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-MiModD_example_workflow_3.ga Wed Feb 11 10:06:13 2015 -0500 |
| [ |
| @@ -0,0 +1,184 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "MiModD example workflow 3", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 172, + "top": 176 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "ref_genome": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "SNAP Read Alignment", + "outputs": [ + { + "name": "outputfile", + "type": "bam" + } + ], + "position": { + "left": 359, + "top": 368 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "read_alignment", + "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"maxhits\\\": \\\"250\\\", \\\"max_mate_overlap\\\": \\\"0\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "list_input_0|inputfile": { + "id": 1, + "output_name": "outputfile" + }, + "ref_genome": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Variant Calling", + "outputs": [ + { + "name": "output_vcf", + "type": "bcf" + } + ], + "position": { + "left": 708, + "top": 364 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "variant_calling", + "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "ifile": { + "id": 2, + "output_name": "output_vcf" + } + }, + "inputs": [], + "name": "Extract Variant Sites", + "outputs": [ + { + "name": "output_vcf", + "type": "vcf" + } + ], + "position": { + "left": 1104.5, + "top": 227 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "extract_variants", + "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "ifile": { + "id": 2, + "output_name": "output_vcf" + } + }, + "inputs": [], + "name": "Coverage Statistics", + "outputs": [ + { + "name": "output_vcf", + "type": "tabular" + } + ], + "position": { + "left": 1133, + "top": 455 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "coverage_stats", + "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "covfile": { + "id": 2, + "output_name": "output_vcf" + }, + "list_input_0|bamfile": { + "id": 1, + "output_name": "outputfile" + } + }, + "inputs": [], + "name": "Deletion Prediction for paired-end data", + "outputs": [ + { + "name": "outputfile", + "type": "gff" + } + ], + "position": { + "left": 1064, + "top": 667 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "deletion_prediction", + "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} |
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| diff -r 000000000000 -r 9f64313f2ccb repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Feb 11 10:06:13 2015 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="These workflows require the mimodd repository."> + <repository changeset_revision="ba685c655e18" name="mimodd" owner="wolma" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories> |