| Previous changeset 0:9f64313f2ccb (2015-02-11) |
|
Commit message:
workflows for MiModD 0.1.6 |
|
modified:
Galaxy-Workflow-MiModD_example_workflow_1.ga Galaxy-Workflow-MiModD_example_workflow_2.ga Galaxy-Workflow-MiModD_example_workflow_3.ga repository_dependencies.xml |
| b |
| diff -r 9f64313f2ccb -r 87bfe31ce878 Galaxy-Workflow-MiModD_example_workflow_1.ga --- a/Galaxy-Workflow-MiModD_example_workflow_1.ga Wed Feb 11 10:06:13 2015 -0500 +++ b/Galaxy-Workflow-MiModD_example_workflow_1.ga Thu Jun 04 18:19:52 2015 +0200 |
| [ |
| @@ -14,6 +14,7 @@ "name": "Input Dataset" } ], + "label": null, "name": "Input dataset", "outputs": [], "position": { @@ -25,7 +26,8 @@ "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "1": { "annotation": "", @@ -37,6 +39,7 @@ } }, "inputs": [], + "label": null, "name": "SNAP Read Alignment", "outputs": [ { @@ -51,10 +54,11 @@ "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_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\\\", \\\"discard_overlapping_mates\\\": \\\"\\\", \\\"maxhits\\\": \\\"250\\\", \\\"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": [] + "user_outputs": [], + "uuid": "None" }, "2": { "annotation": "", @@ -70,6 +74,7 @@ } }, "inputs": [], + "label": null, "name": "Variant Calling", "outputs": [ { @@ -84,10 +89,11 @@ "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_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__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": [] + "user_outputs": [], + "uuid": "None" }, "3": { "annotation": "", @@ -99,6 +105,7 @@ } }, "inputs": [], + "label": null, "name": "Extract Variant Sites", "outputs": [ { @@ -116,7 +123,8 @@ "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "4": { "annotation": "", @@ -128,6 +136,7 @@ } }, "inputs": [], + "label": null, "name": "Coverage Statistics", "outputs": [ { @@ -145,7 +154,8 @@ "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "5": { "annotation": "", @@ -161,6 +171,7 @@ } }, "inputs": [], + "label": null, "name": "Deletion Prediction for paired-end data", "outputs": [ { @@ -169,16 +180,18 @@ } ], "position": { - "left": 1064, - "top": 667 + "left": 1031, + "top": 666 }, "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_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__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": [] + "user_outputs": [], + "uuid": "None" } - } + }, + "uuid": "cd57b671-cca3-4667-8b2a-1e32d0e86d2c" } \ No newline at end of file |
| b |
| diff -r 9f64313f2ccb -r 87bfe31ce878 Galaxy-Workflow-MiModD_example_workflow_2.ga --- a/Galaxy-Workflow-MiModD_example_workflow_2.ga Wed Feb 11 10:06:13 2015 -0500 +++ b/Galaxy-Workflow-MiModD_example_workflow_2.ga Thu Jun 04 18:19:52 2015 +0200 |
| [ |
| @@ -2,7 +2,7 @@ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", - "name": "MiModD example workflow 3", + "name": "MiModD example workflow 2", "steps": { "0": { "annotation": "", @@ -14,6 +14,7 @@ "name": "Input Dataset" } ], + "label": null, "name": "Input dataset", "outputs": [], "position": { @@ -25,7 +26,8 @@ "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "1": { "annotation": "", @@ -37,6 +39,7 @@ } }, "inputs": [], + "label": null, "name": "SNAP Read Alignment", "outputs": [ { @@ -51,10 +54,11 @@ "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}}, {\\\"__index__\\\": 1, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 2, \\\"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_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 1, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 2, \\\"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\\\", \\\"discard_overlapping_mates\\\": \\\"\\\", \\\"maxhits\\\": \\\"250\\\", \\\"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": [] + "user_outputs": [], + "uuid": "None" }, "2": { "annotation": "", @@ -70,6 +74,7 @@ } }, "inputs": [], + "label": null, "name": "Variant Calling", "outputs": [ { @@ -84,10 +89,11 @@ "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_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__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": [] + "user_outputs": [], + "uuid": "None" }, "3": { "annotation": "", @@ -99,6 +105,7 @@ } }, "inputs": [], + "label": null, "name": "Extract Variant Sites", "outputs": [ { @@ -116,7 +123,8 @@ "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "4": { "annotation": "", @@ -128,6 +136,7 @@ } }, "inputs": [], + "label": null, "name": "Coverage Statistics", "outputs": [ { @@ -145,7 +154,8 @@ "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "5": { "annotation": "", @@ -161,6 +171,7 @@ } }, "inputs": [], + "label": null, "name": "Deletion Prediction for paired-end data", "outputs": [ { @@ -175,10 +186,12 @@ "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_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__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": [] + "user_outputs": [], + "uuid": "None" } - } + }, + "uuid": "ebf4ae7e-e823-4b67-a0aa-2a0e70b48db8" } \ No newline at end of file |
| b |
| diff -r 9f64313f2ccb -r 87bfe31ce878 Galaxy-Workflow-MiModD_example_workflow_3.ga --- a/Galaxy-Workflow-MiModD_example_workflow_3.ga Wed Feb 11 10:06:13 2015 -0500 +++ b/Galaxy-Workflow-MiModD_example_workflow_3.ga Thu Jun 04 18:19:52 2015 +0200 |
| [ |
| b'@@ -11,25 +11,52 @@\n "inputs": [\n {\n "description": "", \n- "name": "Input Dataset"\n+ "name": "Reference Genome"\n }\n ], \n+ "label": null, \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 172, \n- "top": 176\n+ "left": 200, \n+ "top": 391\n }, \n "tool_errors": null, \n "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_state": "{\\"name\\": \\"Reference Genome\\"}", \n "tool_version": null, \n "type": "data_input", \n- "user_outputs": []\n+ "user_outputs": [], \n+ "uuid": "None"\n }, \n "1": {\n "annotation": "", \n "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Hawaiian strain variants file"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 707.5, \n+ "top": 335\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Hawaiian strain variants file\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": [], \n+ "uuid": "80c25284-13aa-4172-bb52-2e8adee43626"\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "id": 2, \n "input_connections": {\n "ref_genome": {\n "id": 0, \n@@ -37,6 +64,7 @@\n }\n }, \n "inputs": [], \n+ "label": null, \n "name": "SNAP Read Alignment", \n "outputs": [\n {\n@@ -45,23 +73,24 @@\n }\n ], \n "position": {\n- "left": 359, \n- "top": 368\n+ "left": 334, \n+ "top": 607\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n "tool_id": "read_alignment", \n- "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\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"datasets\\": \\"[{\\\\\\"__index__\\\\\\": 0, \\\\\\"mode_choose\\\\\\": {\\\\\\"input\\\\\\": {\\\\\\"header\\\\\\": null, \\\\\\"ifile\\\\\\": null, \\\\\\"iformat\\\\\\": \\\\\\"bam\\\\\\", \\\\\\"__current_case__\\\\\\": 0}, \\\\\\"mode\\\\\\": \\\\\\"paired\\\\\\", \\\\\\"__current_case__\\\\\\": 1}}, {\\\\\\"__index__\\\\\\": 1, \\\\\\"mode_choose\\\\\\": {\\\\\\"input\\\\\\": {\\\\\\"header\\\\\\": null, \\\\\\"ifile\\\\\\": null, \\\\\\"iformat\\\\\\": \\\\\\"bam\\\\\\", \\\\\\"__current_case__\\\\\\": 0}, \\\\\\"mode\\\\\\": \\\\\\"single\\\\\\", \\\\\\"__current_case__\\\\\\": 0}}]\\", \\"__rerun_remap_job_id__\\": null, \\"set\\": \\"{\\\\\\"sort\\\\\\": \\\\\\"0\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"clipping\\\\\\": \\\\\\"++\\\\\\", \\\\\\"filter_output\\\\\\": \\\\\\"off\\\\'..b' "id": 4, \n+ "id": 5, \n "input_connections": {\n "ifile": {\n- "id": 2, \n+ "id": 3, \n "output_name": "output_vcf"\n }\n }, \n "inputs": [], \n+ "label": null, \n "name": "Coverage Statistics", \n "outputs": [\n {\n@@ -136,8 +174,8 @@\n }\n ], \n "position": {\n- "left": 1133, \n- "top": 455\n+ "left": 1054, \n+ "top": 726\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n@@ -145,40 +183,57 @@\n "tool_state": "{\\"__page__\\": 0, \\"ifile\\": \\"null\\", \\"__rerun_remap_job_id__\\": null}", \n "tool_version": "1.0.0", \n "type": "tool", \n- "user_outputs": []\n+ "user_outputs": [], \n+ "uuid": "None"\n }, \n- "5": {\n+ "6": {\n "annotation": "", \n- "id": 5, \n+ "id": 6, \n "input_connections": {\n- "covfile": {\n- "id": 2, \n+ "ifile": {\n+ "id": 4, \n "output_name": "output_vcf"\n- }, \n- "list_input_0|bamfile": {\n- "id": 1, \n- "output_name": "outputfile"\n }\n }, \n- "inputs": [], \n- "name": "Deletion Prediction for paired-end data", \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool Prepare variant data for mapping", \n+ "name": "sample"\n+ }, \n+ {\n+ "description": "runtime parameter for tool Prepare variant data for mapping", \n+ "name": "run"\n+ }, \n+ {\n+ "description": "runtime parameter for tool Prepare variant data for mapping", \n+ "name": "run"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Prepare variant data for mapping", \n "outputs": [\n {\n- "name": "outputfile", \n- "type": "gff"\n+ "name": "ofile", \n+ "type": "vcf"\n+ }, \n+ {\n+ "name": "dictfile", \n+ "type": "tabular"\n }\n ], \n "position": {\n- "left": 1064, \n- "top": 667\n+ "left": 1209.5, \n+ "top": 200\n }, \n "post_job_actions": {}, \n "tool_errors": null, \n- "tool_id": "deletion_prediction", \n- "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\\\\\\"\\"}", \n+ "tool_id": "cloudmap_prepare", \n+ "tool_state": "{\\"__page__\\": 0, \\"ifile\\": \\"null\\", \\"run\\": \\"{\\\\\\"infer_missing\\\\\\": \\\\\\"False\\\\\\", \\\\\\"related_parent_sample\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, \\\\\\"mode\\\\\\": \\\\\\"VAF\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"unrelated_parent_sample\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}}\\", \\"__rerun_remap_job_id__\\": null, \\"seqdict\\": \\"\\\\\\"True\\\\\\"\\", \\"sample\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n "tool_version": "1.0.0", \n "type": "tool", \n- "user_outputs": []\n+ "user_outputs": [], \n+ "uuid": "6225f501-6db8-4c83-ad42-59a8f1330a55"\n }\n- }\n-}\n+ }, \n+ "uuid": "0a619835-3d93-489f-8d0d-93a567536404"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 9f64313f2ccb -r 87bfe31ce878 repository_dependencies.xml --- a/repository_dependencies.xml Wed Feb 11 10:06:13 2015 -0500 +++ b/repository_dependencies.xml Thu Jun 04 18:19:52 2015 +0200 |
| b |
| @@ -1,4 +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" /> + <repository changeset_revision="ffee8534a5c4" name="mimodd" owner="wolma" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories> |