changeset 4:4de5efbfdb9f draft

Uploaded
author yufei-luo
date Tue, 22 Jan 2013 10:46:11 -0500
parents a07e588f245a
children 143ad8f276e1
files DiffExpAnal/Galaxy-Workflow-Differential_expression_DESeq.ga
diffstat 1 files changed, 510 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DiffExpAnal/Galaxy-Workflow-Differential_expression_DESeq.ga	Tue Jan 22 10:46:11 2013 -0500
@@ -0,0 +1,510 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Differential_expression_DESeq (with replicates)", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "annotation.gff"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 230, 
+                "top": 194.4166717529297
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"annotation.gff\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input replicat 1 for condition 1, fastq format"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 229.9166717529297, 
+                "top": 260.41668701171875
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input replicat 1 for condition 1, fastq format\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input replicat 2 for condition 1, fastq format"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 222.9166717529297, 
+                "top": 316.41668701171875
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input replicat 2 for condition 1, fastq format\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input replicat 1 for condition 2, fastq format"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 222.9166717529297, 
+                "top": 380.41668701171875
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input replicat 1 for condition 2, fastq format\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input replicat 2 for condition 2, fastq format"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 223.9166717529297, 
+                "top": 445.41668701171875
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input replicat 2 for condition 2, fastq format\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input replicat 3 for condition 2, fastq format"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 222.9166717529297, 
+                "top": 511.41668701171875
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input replicat 3 for condition 2, fastq format\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "reference genome .fasta"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 233.0833282470703, 
+                "top": 599
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"reference genome .fasta\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "change gff Features", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gff3"
+                }
+            ], 
+            "position": {
+                "left": 468.5, 
+                "top": 198
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "changeGffFeatures", 
+            "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"gene\\\"\", \"outputFeature\": \"\\\"exon\\\"\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "condition_groups_0|replicates_0|fastq_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }, 
+                "condition_groups_0|replicates_1|fastq_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "condition_groups_1|replicates_0|fastq_file": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "condition_groups_1|replicates_1|fastq_file": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "condition_groups_1|replicates_2|fastq_file": {
+                    "id": 5, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "load_multiFASTQfiles", 
+            "outputs": [
+                {
+                    "name": "multiFASTQfiles_out", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 434.16668701171875, 
+                "top": 312
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "load_multiFASTQ", 
+            "tool_state": "{\"__page__\": 0, \"condition_groups\": \"[{\\\"__index__\\\": 0, \\\"replicates\\\": [{\\\"__index__\\\": 0, \\\"fastq_file\\\": null}, {\\\"__index__\\\": 1, \\\"fastq_file\\\": null}]}, {\\\"__index__\\\": 1, \\\"replicates\\\": [{\\\"__index__\\\": 0, \\\"fastq_file\\\": null}, {\\\"__index__\\\": 1, \\\"fastq_file\\\": null}, {\\\"__index__\\\": 2, \\\"fastq_file\\\": null}]}]\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "formatType|inputFileName": {
+                    "id": 7, 
+                    "output_name": "outputFile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Clean Transcript File", 
+            "outputs": [
+                {
+                    "name": "outputFile", 
+                    "type": "gtf"
+                }
+            ], 
+            "position": {
+                "left": 696.4166870117188, 
+                "top": 255.41668701171875
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "CleanTranscriptFile", 
+            "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "input_file": {
+                    "id": 8, 
+                    "output_name": "multiFASTQfiles_out"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer parallel", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 692.5, 
+                "top": 351.41668701171875
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fastq_groomer_parallel", 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input1": {
+                    "id": 10, 
+                    "output_name": "output_file"
+                }, 
+                "refGenomeSource|ownFile": {
+                    "id": 6, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Tophat parallel for Illumina", 
+                    "name": "tar"
+                }
+            ], 
+            "name": "Tophat parallel for Illumina", 
+            "outputs": [
+                {
+                    "name": "outputFileName", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "outputTarFile", 
+                    "type": "tar"
+                }
+            ], 
+            "position": {
+                "left": 666.1666870117188, 
+                "top": 450
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "tophat_parallel", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"tar\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"singlePaired\": \"{\\\"sParams\\\": {\\\"sSettingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input1": {
+                    "id": 11, 
+                    "output_name": "outputFileName"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool BAM to SAM", 
+                    "name": "header"
+                }, 
+                {
+                    "description": "runtime parameter for tool BAM to SAM", 
+                    "name": "tar"
+                }
+            ], 
+            "name": "BAM to SAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "outputTarFile", 
+                    "type": "tar"
+                }
+            ], 
+            "position": {
+                "left": 927.1666870117188, 
+                "top": 473
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "bam_to_sam_parallel", 
+            "tool_state": "{\"header\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input1\": \"null\", \"tar\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "formatType|inputFileName1": {
+                    "id": 9, 
+                    "output_name": "outputFile"
+                }, 
+                "inputTxt": {
+                    "id": 12, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "CompareOverlapping_parallel", 
+            "outputs": [
+                {
+                    "name": "outTxtFile", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "outputTarFile", 
+                    "type": "tar"
+                }
+            ], 
+            "position": {
+                "left": 897.5, 
+                "top": 314.41668701171875
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "CompareOverlapping_parallel", 
+            "tool_state": "{\"__page__\": 0, \"NotOverlapping\": \"\\\"True\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 1}\", \"InvertMatch\": \"\\\"False\\\"\", \"tar\": \"\\\"False\\\"\", \"ReportIntron\": \"\\\"False\\\"\", \"optionNFirstFile1\": \"{\\\"NFirstForFile1\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionTroisFile2\": \"{\\\"extentionFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionTroisFile1\": \"{\\\"__current_case__\\\": 1, \\\"extentionFile1\\\": \\\"No\\\"}\", \"inputTxt\": \"null\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionCinqFile2\": \"{\\\"extentionFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"MO\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionCinqFile1\": \"{\\\"__current_case__\\\": 1, \\\"extentionFile1\\\": \\\"No\\\"}\", \"OptionColinearOrAntiSens\": \"{\\\"__current_case__\\\": 2, \\\"OptionCA\\\": \\\"NONE\\\"}\", \"format2\": \"\\\"sam\\\"\", \"optionNFirstFile2\": \"{\\\"NFirstForFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionNLastFile2\": \"{\\\"NLastForFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionNLastFile1\": \"{\\\"__current_case__\\\": 1, \\\"NLastForFile1\\\": \\\"No\\\"}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "inputTxt": {
+                    "id": 13, 
+                    "output_name": "outTxtFile"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool countNumber_parallel", 
+                    "name": "tar"
+                }
+            ], 
+            "name": "countNumber_parallel", 
+            "outputs": [
+                {
+                    "name": "outputTxt", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "outputTarFile", 
+                    "type": "tar"
+                }
+            ], 
+            "position": {
+                "left": 1172.5833740234375, 
+                "top": 381
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "countNumber_parallel", 
+            "tool_state": "{\"input\": \"null\", \"inputTxt\": \"null\", \"tar\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "inputFile": {
+                    "id": 14, 
+                    "output_name": "outputTxt"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool DESEQ for differential expression analysis", 
+                    "name": "withOutReplicates"
+                }
+            ], 
+            "name": "DESEQ for differential expression analysis", 
+            "outputs": [
+                {
+                    "name": "outHTML", 
+                    "type": "HTML"
+                }, 
+                {
+                    "name": "outComplete", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outUP", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outDown", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1435.0833740234375, 
+                "top": 350
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "DESEQ", 
+            "tool_state": "{\"__page__\": 0, \"header\": \"\\\"True\\\"\", \"withOutReplicates\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputFile\": \"null\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file