# HG changeset patch
# User urgi-team
# Date 1464269227 14400
# Node ID f8221945b946d3f950f81675cf4a2cb6ca8620ab
# Parent bfd4dc7f50c585f746e03d58dd9cb9049e31e85f
Uploaded
diff -r bfd4dc7f50c5 -r f8221945b946 TEiso/Galaxy-Workflow-TEiso_workflow.ga
--- a/TEiso/Galaxy-Workflow-TEiso_workflow.ga Wed May 25 10:28:25 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,439 +0,0 @@
-{
- "a_galaxy_workflow": "true",
- "annotation": "",
- "format-version": "0.1",
- "name": "TEiso_workflow",
- "steps": {
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- "annotation": "",
- "id": 0,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "Input Dataset"
- }
- ],
- "label": null,
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 200
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- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Input Dataset\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": [],
- "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"
- },
- "1": {
- "annotation": "",
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- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "Input Dataset"
- }
- ],
- "label": null,
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 285
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Input Dataset\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": [],
- "uuid": "98cee5d8-d791-4f91-8f29-ccc98003e392"
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- "label": null,
- "name": "Input dataset",
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- "position": {
- "left": 200,
- "top": 370
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Input Dataset\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": [],
- "uuid": "1fc62c7e-fbb8-48b4-89da-18c629838b7c"
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- "3": {
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- "name": "Input dataset",
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- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Input Dataset\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": [],
- "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"
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- "4": {
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- "id": 4,
- "input_connections": {},
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- "name": "Input Dataset"
- }
- ],
- "label": null,
- "name": "Input dataset",
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- "position": {
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- "top": 540
- },
- "tool_errors": null,
- "tool_id": null,
- "tool_state": "{\"name\": \"Input Dataset\"}",
- "tool_version": null,
- "type": "data_input",
- "user_outputs": [],
- "uuid": "869588d6-af39-40d2-afaa-86a3c9935aa9"
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- "5": {
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- "id": 3,
- "output_name": "output"
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- "singlePaired|input2": {
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- "output_name": "output"
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- "inputs": [],
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- "name": "TopHat",
- "outputs": [
- {
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- "type": "txt"
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- {
- "name": "fusions",
- "type": "tabular"
- },
- {
- "name": "insertions",
- "type": "bed"
- },
- {
- "name": "deletions",
- "type": "bed"
- },
- {
- "name": "junctions",
- "type": "bed"
- },
- {
- "name": "accepted_hits",
- "type": "bam"
- },
- {
- "name": "unmapped",
- "type": "bam"
- }
- ],
- "position": {
- "left": 428,
- "top": 200
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- "post_job_actions": {},
- "tool_errors": null,
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- "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"settingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}",
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- "output_name": "output"
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- "inputs": [],
- "label": null,
- "name": "GFFToBed",
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- "tool_version": "1.0",
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- "inputs": [],
- "label": null,
- "name": "Cufflinks",
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- {
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- },
- {
- "name": "assembled_isoforms",
- "type": "gtf"
- },
- {
- "name": "total_map_mass",
- "type": "txt"
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- ],
- "position": {
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- "top": 200
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- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0",
- "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"min_isoform_fraction\": \"\\\"0.1\\\"\", \"multiread_correct\": \"\\\"No\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"max_intron_len\": \"\\\"300000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"length_correction\": \"\\\"\\\"\", \"advanced_settings\": \"{\\\"__current_case__\\\": 0, \\\"use_advanced_settings\\\": \\\"No\\\"}\"}",
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- "8": {
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- "inputFile": {
- "id": 7,
- "output_name": "assembled_isoforms"
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- },
- "inputs": [],
- "label": null,
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- "type": "bed"
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- "top": 200
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- "post_job_actions": {},
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- "id": 2,
- "output_name": "output"
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- "inputs": {
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- "output_name": "skipped"
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- "id": 3,
- "output_name": "output"
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- },
- "inputs": [],
- "label": null,
- "name": "Cuffcompare",
- "outputs": [
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- "type": "txt"
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- "name": "input2_tmap",
- "type": "tabular"
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- "type": "tabular"
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- "position": {
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- "top": 716
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- "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0",
- "tool_state": "{\"seq_data\": \"{\\\"use_seq_data\\\": \\\"Yes\\\", \\\"seq_source\\\": {\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1}\", \"inputs\": \"null\", \"max_dist_group\": \"\\\"100\\\"\", \"__page__\": 0, \"discard_intron_redundant_transfrags\": \"\\\"False\\\"\", \"max_dist_exon\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"additional_inputs\": \"[]\", \"discard_single_exon\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"annotation\": \"{\\\"reference_annotation\\\": null, \\\"use_ref_annotation\\\": \\\"Yes\\\", \\\"ignore_nonoverlapping_reference\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"ignore_nonoverlapping_transfrags\\\": \\\"False\\\"}\"}",
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- "inputB": {
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- "label": null,
- "name": "ClosestBed",
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- {
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- "type": "bed"
- }
- ],
- "position": {
- "left": 1436,
- "top": 303
- },
- "post_job_actions": {},
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.24.0",
- "tool_state": "{\"__page__\": 0, \"addition\": \"\\\"True\\\"\", \"k\": \"\\\"1\\\"\", \"inputB\": \"null\", \"mdb\": \"\\\"each\\\"\", \"inputA\": \"null\", \"io\": \"\\\"False\\\"\", \"ties\": \"\\\"all\\\"\", \"addition2\": \"{\\\"fu\\\": \\\"False\\\", \\\"iu\\\": \\\"False\\\", \\\"fd\\\": \\\"False\\\", \\\"__current_case__\\\": 2, \\\"addition2_select\\\": \\\"a\\\", \\\"id\\\": \\\"False\\\"}\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"strand\": \"\\\"\\\"\"}",
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- "input_connections": {
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- "label": null,
- "name": "ClosestToStartSite",
- "outputs": [
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- "uuid": "ad643964-b679-41d0-a74f-e712a8550c7f"
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\ No newline at end of file
diff -r bfd4dc7f50c5 -r f8221945b946 TEiso/repository_dependencies.xml
--- a/TEiso/repository_dependencies.xml Wed May 25 10:28:25 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-
-
-
-
-
-
-
diff -r bfd4dc7f50c5 -r f8221945b946 Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga Thu May 26 09:27:07 2016 -0400
@@ -0,0 +1,439 @@
+{
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+ "annotation": "",
+ "format-version": "0.1",
+ "name": "TEiso_workflow",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 200
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": [],
+ "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"
+ },
+ "1": {
+ "annotation": "",
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 285
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": [],
+ "uuid": "98cee5d8-d791-4f91-8f29-ccc98003e392"
+ },
+ "2": {
+ "annotation": "",
+ "id": 2,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 370
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": [],
+ "uuid": "1fc62c7e-fbb8-48b4-89da-18c629838b7c"
+ },
+ "3": {
+ "annotation": "",
+ "id": 3,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
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+ "top": 455
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": [],
+ "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"
+ },
+ "4": {
+ "annotation": "",
+ "id": 4,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 540
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": [],
+ "uuid": "869588d6-af39-40d2-afaa-86a3c9935aa9"
+ },
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+ "input_connections": {
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+ "output_name": "output"
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+ "id": 1,
+ "output_name": "output"
+ }
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+ "inputs": [],
+ "label": null,
+ "name": "TopHat",
+ "outputs": [
+ {
+ "name": "align_summary",
+ "type": "txt"
+ },
+ {
+ "name": "fusions",
+ "type": "tabular"
+ },
+ {
+ "name": "insertions",
+ "type": "bed"
+ },
+ {
+ "name": "deletions",
+ "type": "bed"
+ },
+ {
+ "name": "junctions",
+ "type": "bed"
+ },
+ {
+ "name": "accepted_hits",
+ "type": "bam"
+ },
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+ "type": "bam"
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+ ],
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+ "top": 200
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+ "inputs": [],
+ "label": null,
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+ "outputs": [
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+ "type": "bed"
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+ "top": 535
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+ "post_job_actions": {},
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+ "7": {
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+ "label": null,
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+ "type": "tabular"
+ },
+ {
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+ },
+ {
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\ No newline at end of file
diff -r bfd4dc7f50c5 -r f8221945b946 Teiso-workflow-final/repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Teiso-workflow-final/repository_dependencies.xml Thu May 26 09:27:07 2016 -0400
@@ -0,0 +1,7 @@
+
+
+
+
+
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+