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changeset 2:ea2117a7b363 draft

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Uploaded CAPS marker design workflow for 454 Data
author john-mccallum
date Sun, 09 Sep 2012 23:16:56 -0400
parents a0689dc29b7f
children 402c3f0fe807
files Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga
diffstat 1 files changed, 401 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga	Sun Sep 09 23:16:56 2012 -0400
@@ -0,0 +1,401 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "CAPS Marker Development from 454 Read Mapping", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference sequences"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 122.80303955078125, 
+                "top": 119.77274131774902
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference sequences\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "Reads to map", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "Reads to map", 
+                    "name": "SFF File "
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 104.6212158203125, 
+                "top": 313.95454406738281
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"SFF File \"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "barcode, vector or adapter sequences to trim", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "barcode, vector or adapter sequences to trim", 
+                    "name": "Trimming file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 195.727294921875, 
+                "top": 544.8787841796875
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Trimming file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
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+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "sff_inputs_0|sff_input": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "vt": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "runMapping", 
+            "outputs": [
+                {
+                    "name": "newbler_metrics", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "read_status", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "trimmed_reads_fasta", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "trimmed_reads_qual", 
+                    "type": "qual454"
+                }, 
+                {
+                    "name": "alignment_info", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "all_contigs_fasta", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "all_contigs_qual", 
+                    "type": "qual454"
+                }, 
+                {
+                    "name": "contigs_ace", 
+                    "type": "ace"
+                }, 
+                {
+                    "name": "large_contigs_fasta", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "large_contigs_qual", 
+                    "type": "qual454"
+                }, 
+                {
+                    "name": "pair_align", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "pair_status", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "scaffolds_fasta", 
+                    "type": "fasta"
+                }, 
+                {
+                    "name": "scaffolds_qual", 
+                    "type": "qual454"
+                }, 
+                {
+                    "name": "scaffolds_agp", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "tag_pair_align", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "trim_status", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "all_diffs", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "all_struct_vars", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "hc_diff", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "hc_struct_vars", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "gene_status", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "mapping_qc", 
+                    "type": "xls"
+                }, 
+                {
+                    "name": "ref_status", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 432.71212768554688, 
+                "top": 330.90908813476562
+            }, 
+            "post_job_actions": {}, 
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+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "inputGsFile": {
+                    "id": 3, 
+                    "output_name": "all_diffs"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Convert gsMapper to gff3", 
+            "outputs": [
+                {
+                    "name": "outputfile", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 729.65148448944092, 
+                "top": 503.80300903320312
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+            "post_job_actions": {}, 
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+            "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/gsMapper_to_gff3_1/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"inputGsFile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
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+                    "output_name": "output"
+                }, 
+                "inputSNPGff3File": {
+                    "id": 4, 
+                    "output_name": "outputfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "CAPS Detection", 
+            "outputs": [
+                {
+                    "name": "outputfile", 
+                    "type": "interval"
+                }
+            ], 
+            "position": {
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+            "tool_state": "{\"inputFasta\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputSNPGff3File\": \"null\", \"__page__\": 0}", 
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+                    "output_name": "outputfile"
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+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
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+            "tool_state": "{\"columnList\": \"\\\"c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
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+            "type": "tool", 
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+                    "name": "min_size"
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+                {
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+                    "name": "max_size"
+                }
+            ], 
+            "name": "Design primers to features", 
+            "outputs": [
+                {
+                    "name": "primer_outputfile", 
+                    "type": "tabular"
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+            ], 
+            "position": {
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+        "8": {
+            "annotation": "Select successful design targets", 
+            "id": 8, 
+            "input_connections": {
+                "input": {
+                    "id": 7, 
+                    "output_name": "primer_outputfile"
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+            "inputs": [], 
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+            "outputs": [
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+                    "type": "input"
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+            "input_connections": {
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+                    "output_name": "out_file1"
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+            "inputs": [], 
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+    }
+}
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