Mercurial > repos > getiria-onsongo > assessing_target_enrichment

changeset 1:ae6eb099d5b8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author getiria-onsongo
date Thu, 06 Dec 2012 12:27:49 -0500
parents dbd0bf3cc3f6
children e511eb3c39c3
files BamExonCoverage1X10X20X30X.ga
diffstat 1 files changed, 450 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BamExonCoverage1X10X20X30X.ga	Thu Dec 06 12:27:49 2012 -0500
@@ -0,0 +1,450 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "BamExonCoverage1X10X20X30X", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "mapped reads: .BAM"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 197.4166259765625, 
+                "top": 357.41667175292969
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"mapped reads: .BAM\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "targeted interval: .bed"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 1202, 
+                "top": 778
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"targeted interval: .bed\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 454, 
+                "top": 237
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "samtools_mpileup", 
+            "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input": {
+                    "id": 2, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Compute", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 727, 
+                "top": 372
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Add_a_column1", 
+            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2-1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"round\": \"\\\"yes\\\"\", \"input\": \"null\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input": {
+                    "id": 3, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 963, 
+                "top": 322
+            }, 
+            "post_job_actions": {
+                "ChangeDatatypeActionout_file1": {
+                    "action_arguments": {
+                        "newtype": "interval"
+                    }, 
+                    "action_type": "ChangeDatatypeAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"columnList\": \"\\\"c1,c7,c2,c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input": {
+                    "id": 4, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1184, 
+                "top": 422
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Filter1", 
+            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 1\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "input1": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input2": {
+                    "id": 5, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Coverage", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "interval"
+                }
+            ], 
+            "position": {
+                "left": 1485, 
+                "top": 422
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "gops_coverage_1", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "input": {
+                    "id": 5, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1439, 
+                "top": 608
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Filter1", 
+            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 10\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input1": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input2": {
+                    "id": 7, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Coverage", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "interval"
+                }
+            ], 
+            "position": {
+                "left": 1699, 
+                "top": 614
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "gops_coverage_1", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "input": {
+                    "id": 7, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1718, 
+                "top": 773
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Filter1", 
+            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 20\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "input1": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input2": {
+                    "id": 9, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Coverage", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "interval"
+                }
+            ], 
+            "position": {
+                "left": 1944, 
+                "top": 773
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "gops_coverage_1", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input": {
+                    "id": 9, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1922, 
+                "top": 976
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Filter1", 
+            "tool_state": "{\"input\": \"null\", \"cond\": \"\\\"c4 >= 30\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input1": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "input2": {
+                    "id": 11, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Coverage", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "interval"
+                }
+            ], 
+            "position": {
+                "left": 2158, 
+                "top": 977
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "gops_coverage_1", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "file_chooser_0|input": {
+                    "id": 10, 
+                    "output_name": "output"
+                }, 
+                "file_chooser_1|input": {
+                    "id": 12, 
+                    "output_name": "output"
+                }, 
+                "input1": {
+                    "id": 6, 
+                    "output_name": "output"
+                }, 
+                "input2": {
+                    "id": 8, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Column Join", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 2387, 
+                "top": 474
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "Coverage1X10X20X30X"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "column_join", 
+            "tool_state": "{\"input2\": \"null\", \"hinge\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"input1\": \"null\", \"__page__\": 0, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"file_chooser\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}]\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\", \\\"2\\\", \\\"3\\\", \\\"5\\\"]}\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file