# HG changeset patch # User Wolfgang Maier # Date 1433434792 -7200 # Node ID 87bfe31ce878d1e3eb4f43866c0840758e94fe87 # Parent 9f64313f2ccb494ec7133c21c8421c268a9ec498 workflows for MiModD 0.1.6 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 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 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 @@ -11,25 +11,52 @@ "inputs": [ { "description": "", - "name": "Input Dataset" + "name": "Reference Genome" } ], + "label": null, "name": "Input dataset", "outputs": [], "position": { - "left": 172, - "top": 176 + "left": 200, + "top": 391 }, "tool_errors": null, "tool_id": null, - "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_state": "{\"name\": \"Reference Genome\"}", "tool_version": null, "type": "data_input", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, "1": { "annotation": "", "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hawaiian strain variants file" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 707.5, + "top": 335 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Hawaiian strain variants file\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [], + "uuid": "80c25284-13aa-4172-bb52-2e8adee43626" + }, + "2": { + "annotation": "", + "id": 2, "input_connections": { "ref_genome": { "id": 0, @@ -37,6 +64,7 @@ } }, "inputs": [], + "label": null, "name": "SNAP Read Alignment", "outputs": [ { @@ -45,23 +73,24 @@ } ], "position": { - "left": 359, - "top": 368 + "left": 334, + "top": 607 }, "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}}, {\\\"__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\\\", \\\"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": { + "3": { "annotation": "", - "id": 2, + "id": 3, "input_connections": { "list_input_0|inputfile": { - "id": 1, + "id": 2, "output_name": "outputfile" }, "ref_genome": { @@ -70,6 +99,7 @@ } }, "inputs": [], + "label": null, "name": "Variant Calling", "outputs": [ { @@ -78,27 +108,33 @@ } ], "position": { - "left": 708, - "top": 364 + "left": 692, + "top": 607 }, "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": { + "4": { "annotation": "", - "id": 3, + "id": 4, "input_connections": { "ifile": { - "id": 2, + "id": 3, "output_name": "output_vcf" + }, + "sitesinfo_0|pre_vcf": { + "id": 1, + "output_name": "output" } }, "inputs": [], + "label": null, "name": "Extract Variant Sites", "outputs": [ { @@ -107,27 +143,29 @@ } ], "position": { - "left": 1104.5, - "top": 227 + "left": 973.5, + "top": 483 }, "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_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[{\\\"__index__\\\": 0, \\\"pre_vcf\\\": null}]\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "user_outputs": [] + "user_outputs": [], + "uuid": "None" }, - "4": { + "5": { "annotation": "", - "id": 4, + "id": 5, "input_connections": { "ifile": { - "id": 2, + "id": 3, "output_name": "output_vcf" } }, "inputs": [], + "label": null, "name": "Coverage Statistics", "outputs": [ { @@ -136,8 +174,8 @@ } ], "position": { - "left": 1133, - "top": 455 + "left": 1054, + "top": 726 }, "post_job_actions": {}, "tool_errors": null, @@ -145,40 +183,57 @@ "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": { + "6": { "annotation": "", - "id": 5, + "id": 6, "input_connections": { - "covfile": { - "id": 2, + "ifile": { + "id": 4, "output_name": "output_vcf" - }, - "list_input_0|bamfile": { - "id": 1, - "output_name": "outputfile" } }, - "inputs": [], - "name": "Deletion Prediction for paired-end data", + "inputs": [ + { + "description": "runtime parameter for tool Prepare variant data for mapping", + "name": "sample" + }, + { + "description": "runtime parameter for tool Prepare variant data for mapping", + "name": "run" + }, + { + "description": "runtime parameter for tool Prepare variant data for mapping", + "name": "run" + } + ], + "label": null, + "name": "Prepare variant data for mapping", "outputs": [ { - "name": "outputfile", - "type": "gff" + "name": "ofile", + "type": "vcf" + }, + { + "name": "dictfile", + "type": "tabular" } ], "position": { - "left": 1064, - "top": 667 + "left": 1209.5, + "top": 200 }, "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_id": "cloudmap_prepare", + "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\\\"}\"}", "tool_version": "1.0.0", "type": "tool", - "user_outputs": [] + "user_outputs": [], + "uuid": "6225f501-6db8-4c83-ad42-59a8f1330a55" } - } -} + }, + "uuid": "0a619835-3d93-489f-8d0d-93a567536404" +} \ No newline at end of file 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 @@ -1,4 +1,4 @@ - +