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changeset 5:af119bf658e8 draft

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Uploaded
author scisjnu123
date Thu, 12 Sep 2019 12:38:04 -0400
parents abdb3ed0c740
children ebc5e82e6ae5
files Galaxy-Workflow-VARSCAN.ga
diffstat 1 files changed, 133 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-VARSCAN.ga	Thu Sep 12 12:38:04 2019 -0400
@@ -0,0 +1,133 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "This workflow call SNPs, INDELs and CNSs.", 
+    "format-version": "0.1", 
+    "name": "VARSCAN", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": ".bam file."
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 135
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \".bam file.\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "f0436072-1b25-459c-ad0b-a9e5379bcb93"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference genome."
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 202.5, 
+                "top": 211
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference genome.\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "197c41ff-2653-4195-b961-d6e0444a8c73"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "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": 444.5, 
+                "top": 141
+            }, 
+            "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": "da60e628-cc66-417a-8419-d0ada8df76e0"
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "in_file": {
+                    "id": 2, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "VarScan mpileup", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "vcf"
+                }, 
+                {
+                    "name": "log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 710.5, 
+                "top": 190
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_mpileup/2.3.5", 
+            "tool_state": "{\"strand_filter\": \"\\\"1\\\"\", \"min_avg_qual\": \"\\\"15\\\"\", \"min_coverage\": \"\\\"8\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"min_freq_for_hom\": \"\\\"0.75\\\"\", \"min_var_freq\": \"\\\"0.01\\\"\", \"exe_command\": \"\\\"mpileup2snp\\\"\", \"min_reads2\": \"\\\"2\\\"\", \"p_value\": \"\\\"0.99\\\"\", \"variants\": \"\\\"1\\\"\", \"vcf_sample_list\": \"null\", \"in_file\": \"null\"}", 
+            "tool_version": "2.3.5", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "ad908d2b-e0dc-4742-8c03-e612aab136aa"
+        }
+    }, 
+    "uuid": "cd50a688-f133-497a-94b5-974f6c41af9e"
+}
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