changeset 2:d60e070af736 draft

Shorten workflow file name
author stemcellcommons
date Thu, 28 Apr 2016 17:04:04 -0400
parents f260bd09f529
children cfae7747e902
files Galaxy-Workflow-TF_ChIP-Seq_analysis_using_MACS2__hg19.ga TF_ChIP-Seq_analysis_using_MACS2__hg19.ga
diffstat 2 files changed, 387 insertions(+), 387 deletions(-) [+]
line wrap: on
line diff
--- a/Galaxy-Workflow-TF_ChIP-Seq_analysis_using_MACS2__hg19.ga	Thu Apr 28 12:32:15 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,387 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}", 
-    "format-version": "0.1", 
-    "name": "TF ChIP-Seq analysis using MACS2: hg19", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "exp_file"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 206, 
-                "top": 381.265625
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"exp_file\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "input_file"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 201, 
-                "top": 516.265625
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"input_file\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {
-                "input_file": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "FASTQ Parallel Groomer", 
-            "outputs": [
-                {
-                    "name": "output_file", 
-                    "type": "fastqsanger"
-                }
-            ], 
-            "position": {
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-                "top": 341.265625
-            }, 
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-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
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-            "outputs": [
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-                    "name": "output_file", 
-                    "type": "fastqsanger"
-                }
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-                "top": 493.265625
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-            "type": "tool", 
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-                    "output_name": "output_file"
-                }
-            }, 
-            "inputs": [], 
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-            "outputs": [
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-                }, 
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-                    "type": "fastq"
-                }, 
-                {
-                    "name": "output_suppressed_reads_r", 
-                    "type": "fastq"
-                }, 
-                {
-                    "name": "output_unmapped_reads_l", 
-                    "type": "fastq"
-                }, 
-                {
-                    "name": "output_unmapped_reads_r", 
-                    "type": "fastq"
-                }
-            ], 
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-                    "output_name": "output"
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-                    "output_name": "outfile"
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-            "outputs": [
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga	Thu Apr 28 17:04:04 2016 -0400
@@ -0,0 +1,387 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}", 
+    "format-version": "0.1", 
+    "name": "TF ChIP-Seq analysis using MACS2: hg19", 
+    "steps": {
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+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "exp_file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 206, 
+                "top": 381.265625
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"exp_file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "input_file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 201, 
+                "top": 516.265625
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"input_file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Parallel Groomer", 
+            "outputs": [
+                {
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+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
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+                "top": 341.265625
+            }, 
+            "post_job_actions": {}, 
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+            "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
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+            "type": "tool", 
+            "user_outputs": []
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+            "input_connections": {
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+                    "output_name": "output"
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+            "inputs": [], 
+            "name": "FASTQ Parallel Groomer", 
+            "outputs": [
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+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
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+                "top": 493.265625
+            }, 
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+            "tool_version": "0.3.1", 
+            "type": "tool", 
+            "user_outputs": []
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+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "singlePaired|sInput1": {
+                    "id": 2, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with Bowtie for Illumina", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "sam"
+                }, 
+                {
+                    "name": "output_suppressed_reads_l", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_suppressed_reads_r", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_unmapped_reads_l", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_unmapped_reads_r", 
+                    "type": "fastq"
+                }
+            ], 
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+                "left": 755.5, 
+                "top": 272.265625
+            }, 
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