changeset 7:ab331b4507fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-SAMTools.ga	Thu Sep 12 12:39:24 2019 -0400
@@ -0,0 +1,129 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "This workflow uses SAMTools to call SNPs and INDELs.", 
+    "format-version": "0.1", 
+    "name": "SAMTools", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": ".bam file"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 156
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \".bam file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "955f71da-3fad-46c4-a1d9-b0b1cb484569"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference genome."
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 512, 
+                "top": 285
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference genome.\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "7069b8d2-a89a-472a-8e18-b5b8f076de33"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "SortSam", 
+            "outputs": [
+                {
+                    "name": "outFile", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 436.5, 
+                "top": 121
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_SortSam/1.135", 
+            "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"coordinate\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", 
+            "tool_version": "1.135", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "b06955b6-6bba-4aaa-a919-fbb2aba9fdf5"
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 2, 
+                    "output_name": "outFile"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 746, 
+                "top": 192
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "99b58983-e355-4357-b77e-8e29afcdc866"
+        }
+    }, 
+    "uuid": "6b217aca-887a-4cca-91e4-446a7cc50726"
+}
\ No newline at end of file