Repository 'rnaseq_workflows'
hg clone https://toolshed.g2.bx.psu.edu/repos/stemcellcommons/rnaseq_workflows

Changeset 0:cbd6667ca478 (2016-07-20)
Next changeset 1:ba1b76257fa5 (2016-07-21)
Commit message:
Initial upload
added:
RNA-seq_paired_end_with_TopHat_-_hg19.ga
RNA-seq_paired_end_with_TopHat_-_mm10.ga
RNA-seq_single_end_with_TopHat_-_hg19.ga
RNA-seq_single_end_with_TopHat_-_mm10.ga
b
diff -r 000000000000 -r cbd6667ca478 RNA-seq_paired_end_with_TopHat_-_hg19.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNA-seq_paired_end_with_TopHat_-_hg19.ga Wed Jul 20 16:58:05 2016 -0400
[
b'@@ -0,0 +1,281 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "{\\"refinery_type\\": \\"analysis\\", \\"refinery_relationships\\": [{\\"category\\": \\"1-1\\", \\"set1\\": \\"forward_reads\\", \\"set2\\": \\"reverse_reads\\"}]}", \n+    "format-version": "0.1", \n+    "name": "RNA-seq paired end with TopHat - hg19", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "forward_reads"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 207, \n+                "top": 300\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"forward_reads\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", \n+            "workflow_outputs": []\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "reverse_reads"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 205, \n+                "top": 437\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"reverse_reads\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "d2dbe3db-13ca-4155-a60a-cf408e53cb3a", \n+            "workflow_outputs": []\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 2, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position": {\n+                "left": 455.5, \n+                "top": 259\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"options_type_selector\\\\\\": \\\\\\"basic\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.3.1", \n+            "type": "tool", \n+            "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", \n+            "workflow_outputs": []\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 3, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 1, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position"'..b'"paired\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"mate_inner_distance\\\\\\": \\\\\\"300\\\\\\", \\\\\\"mate_std_dev\\\\\\": \\\\\\"20\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"readGroup\\": \\"{\\\\\\"__current_case__\\\\\\": 1, \\\\\\"specReadGroup\\\\\\": \\\\\\"no\\\\\\"}\\", \\"params\\": \\"{\\\\\\"min_intron_length\\\\\\": \\\\\\"70\\\\\\", \\\\\\"min_segment_intron\\\\\\": \\\\\\"50\\\\\\", \\\\\\"fusion_search\\\\\\": {\\\\\\"__current_case__\\\\\\": 0, \\\\\\"do_search\\\\\\": \\\\\\"No\\\\\\"}, \\\\\\"seg_mismatches\\\\\\": \\\\\\"2\\\\\\", \\\\\\"library_type\\\\\\": \\\\\\"fr-unstranded\\\\\\", \\\\\\"settingsType\\\\\\": \\\\\\"full\\\\\\", \\\\\\"coverage_search\\\\\\": {\\\\\\"use_search\\\\\\": \\\\\\"No\\\\\\", \\\\\\"__current_case__\\\\\\": 2}, \\\\\\"splice_mismatches\\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b
diff -r 000000000000 -r cbd6667ca478 RNA-seq_paired_end_with_TopHat_-_mm10.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNA-seq_paired_end_with_TopHat_-_mm10.ga Wed Jul 20 16:58:05 2016 -0400
[
b'@@ -0,0 +1,281 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "{\\"refinery_type\\": \\"analysis\\", \\"refinery_relationships\\": [{\\"category\\": \\"1-1\\", \\"set1\\": \\"forward_reads\\", \\"set2\\": \\"reverse_reads\\"}]}", \n+    "format-version": "0.1", \n+    "name": "RNA-seq paired end with TopHat - mm10", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "forward_reads"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 207, \n+                "top": 300\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"forward_reads\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "13ea8b03-730c-404a-8fd9-93ca91175447", \n+            "workflow_outputs": []\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "reverse_reads"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 205, \n+                "top": 437\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"reverse_reads\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "uuid": "d2dbe3db-13ca-4155-a60a-cf408e53cb3a", \n+            "workflow_outputs": []\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 2, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position": {\n+                "left": 455.5, \n+                "top": 259\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "tool_state": "{\\"__page__\\": 0, \\"input_type\\": \\"\\\\\\"sanger\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"options_type\\": \\"{\\\\\\"options_type_selector\\\\\\": \\\\\\"basic\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.3.1", \n+            "type": "tool", \n+            "uuid": "e969943f-2c34-4aa4-a8a2-89ea2179b641", \n+            "workflow_outputs": []\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", \n+            "id": 3, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 1, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Parallel Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position"'..b'"paired\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"mate_inner_distance\\\\\\": \\\\\\"300\\\\\\", \\\\\\"mate_std_dev\\\\\\": \\\\\\"20\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"readGroup\\": \\"{\\\\\\"__current_case__\\\\\\": 1, \\\\\\"specReadGroup\\\\\\": \\\\\\"no\\\\\\"}\\", \\"params\\": \\"{\\\\\\"min_intron_length\\\\\\": \\\\\\"70\\\\\\", \\\\\\"min_segment_intron\\\\\\": \\\\\\"50\\\\\\", \\\\\\"fusion_search\\\\\\": {\\\\\\"__current_case__\\\\\\": 0, \\\\\\"do_search\\\\\\": \\\\\\"No\\\\\\"}, \\\\\\"seg_mismatches\\\\\\": \\\\\\"2\\\\\\", \\\\\\"library_type\\\\\\": \\\\\\"fr-unstranded\\\\\\", \\\\\\"settingsType\\\\\\": \\\\\\"full\\\\\\", \\\\\\"coverage_search\\\\\\": {\\\\\\"use_search\\\\\\": \\\\\\"No\\\\\\", \\\\\\"__current_case__\\\\\\": 2}, \\\\\\"splice_mismatches\\\\\\": \\\\\\"0\\\\\\", \\\\\\"max_multihits\\\\\\": \\\\\\"20\\\\\\", \\\\\\"bowtie_n\\\\\\": \\\\\\"No\\\\\\", \\\\\\"read_realign_edit_dist\\\\\\": \\\\\\"1000\\\\\\", \\\\\\"max_intron_length\\\\\\": \\\\\\"500000\\\\\\", \\\\\\"anchor_length\\\\\\": \\\\\\"8\\\\\\", \\\\\\"microexon_search\\\\\\": \\\\\\"No\\\\\\", \\\\\\"indel_search\\\\\\": {\\\\\\"max_insertion_length\\\\\\": \\\\\\"3\\\\\\", \\\\\\"max_deletion_length\\\\\\": \\\\\\"3\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"allow_indel_search\\\\\\": \\\\\\"Yes\\\\\\"}, \\\\\\"read_edit_dist\\\\\\": \\\\\\"2\\\\\\", \\\\\\"output_unmapped\\\\\\": \\\\\\"False\\\\\\", \\\\\\"own_junctions\\\\\\": {\\\\\\"gene_model_ann\\\\\\": {\\\\\\"gene_annotation_model\\\\\\": \\\\\\"mm10_genes.gtf\\\\\\", \\\\\\"use_annotations\\\\\\": \\\\\\"indexed\\\\\\", \\\\\\"__current_case__\\\\\\": 1}, \\\\\\"no_novel_juncs\\\\\\": \\\\\\"No\\\\\\", \\\\\\"use_junctions\\\\\\": \\\\\\"Yes\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"raw_juncs\\\\\\": {\\\\\\"use_juncs\\\\\\": \\\\\\"No\\\\\\", \\\\\\"__current_case__\\\\\\": 0}}, \\\\\\"seg_length\\\\\\": \\\\\\"25\\\\\\", \\\\\\"max_segment_intron\\\\\\": \\\\\\"500000\\\\\\", \\\\\\"bowtie2_settings\\\\\\": {\\\\\\"__current_case__\\\\\\": 0, \\\\\\"b2_settings\\\\\\": \\\\\\"No\\\\\\"}, \\\\\\"__current_case__\\\\\\": 1, \\\\\\"read_mismatches\\\\\\": \\\\\\"2\\\\\\"}\\", \\"refGenomeSource\\": \\"{\\\\\\"genomeSource\\\\\\": \\\\\\"indexed\\\\\\", \\\\\\"index\\\\\\": \\\\\\"mm10\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+            "tool_version": "2.1.0", \n+            "type": "tool", \n+            "uuid": "9f2be90e-a62e-4d50-91a1-00171e11baa5", \n+            "workflow_outputs": []\n+        }, \n+        "6": {\n+            "annotation": "{\\n\\"output\\": {\\n\\"name\\": \\"feature_counts\\", \\"description\\": \\"\\",\\n\\"type\\": \\"tabular\\"\\n},\\n\\"output_summary\\": {\\n\\"name\\": \\"feature_counts_summary\\", \\"description\\": \\"\\",\\n\\"type\\": \\"tabular\\"\\n}\\n}", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", \n+            "id": 6, \n+            "input_connections": {\n+                "alignments": {\n+                    "id": 5, \n+                    "output_name": "accepted_hits"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "featureCounts", \n+            "outputs": [\n+                {\n+                    "name": "output", \n+                    "type": "tabular"\n+                }, \n+                {\n+                    "name": "output_summary", \n+                    "type": "tabular"\n+                }\n+            ], \n+            "position": {\n+                "left": 1441, \n+                "top": 388\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5", \n+            "tool_state": "{\\"__page__\\": 0, \\"reference_gene_sets_source\\": \\"{\\\\\\"reference_gene_sets\\\\\\": \\\\\\"/mnt/galaxyIndices/gene_annotations/mm10_genes.gtf\\\\\\", \\\\\\"__current_case__\\\\\\": 2, \\\\\\"source_select\\\\\\": \\\\\\"indexed_all\\\\\\"}\\", \\"format\\": \\"\\\\\\"tabdel_short\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"alignments\\": \\"null\\", \\"extended_parameters\\": \\"{\\\\\\"parameters\\\\\\": \\\\\\"default\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+            "tool_version": "1.4.6.p5", \n+            "type": "tool", \n+            "uuid": "39697dc6-5c56-4f5c-be9c-354197ee77dd", \n+            "workflow_outputs": []\n+        }\n+    }, \n+    "uuid": "b8caaaab-6755-4be2-9b28-d16c66777751"\n+}\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r cbd6667ca478 RNA-seq_single_end_with_TopHat_-_hg19.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNA-seq_single_end_with_TopHat_-_hg19.ga Wed Jul 20 16:58:05 2016 -0400
[
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b
diff -r 000000000000 -r cbd6667ca478 RNA-seq_single_end_with_TopHat_-_mm10.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNA-seq_single_end_with_TopHat_-_mm10.ga Wed Jul 20 16:58:05 2016 -0400
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