# HG changeset patch
# User wolma
# Date 1423667173 18000
# Node ID 9f64313f2ccb494ec7133c21c8421c268a9ec498

Uploaded

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
@@ -0,0 +1,184 @@
+{
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+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "MiModD example workflow 1", 
+    "steps": {
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+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
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+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
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+                "top": 176
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
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+            "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
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+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "read_alignment", 
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+            "type": "tool", 
+            "user_outputs": []
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+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Variant Calling", 
+            "outputs": [
+                {
+                    "name": "output_vcf", 
+                    "type": "bcf"
+                }
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+                "top": 364
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+                    "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"
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+            }, 
+            "inputs": [], 
+            "name": "Coverage Statistics", 
+            "outputs": [
+                {
+                    "name": "output_vcf", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1133, 
+                "top": 455
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+            "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"
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+                "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
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
@@ -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__\\\": 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_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": 362
+            }, 
+            "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": 225
+            }, 
+            "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": 453
+            }, 
+            "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": []
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+            "id": 5, 
+            "input_connections": {
+                "covfile": {
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+                    "output_name": "output_vcf"
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+                "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": 665
+            }, 
+            "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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+}
\ No newline at end of file
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": []
+        }, 
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+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
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+                    "id": 1, 
+                    "output_name": "outputfile"
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+                "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": []
+        }
+    }
+}
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
@@ -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>