changeset 0:9d5e59373c84

Initial upload
author Jim Johnson <jj@umn.edu>
date Mon, 17 Mar 2014 16:03:12 -0500
parents
children 20d9fb1ba210
files README.rst proteomics_rnaseq_reduced_db_workflow.ga repository_dependencies.xml
diffstat 3 files changed, 746 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Mar 17 16:03:12 2014 -0500
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+This package contains a Galaxy workflow that reduces a reference protein sequence database by retaining only the sequences that are detected at significant levels in the RNA-seq sample.
+The workflow uses RSEM to quantify transcripts in an RNA-seq sample.
+
+See http://www.galaxyproject.org for information about the Galaxy Project.
+
+
+Availability
+============
+
+This workflow is available to download and/or install from the main
+Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_reduced_db_workflow
+
+
+Reference Data
+==============
+
+For Human RNAseq data this workflow was tested using reference data from:
+
+* ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.chromosome.[1-9XY]*.fa.gz
+* ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz
+* ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz
+
+
+For Mouse RNAseq data this workflow was tested using reference data from:
+
+* ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.chromosome.[1-9XY]*.fa.gz
+* ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz
+* ftp://ftp.ensembl.org/pub/release-73/gtf/mus_musculus/Mus_musculus.GRCm38.73.gtf.gz
+
+
+
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view//jjohnson/rsem
+* http://toolshed.g2.bx.psu.edu/view/devteam/fasta_formatter
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial release to Tool Shed (March, 2014)
+======= ======================================================================
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteomics_rnaseq_reduced_db_workflow.ga	Mon Mar 17 16:03:12 2014 -0500
@@ -0,0 +1,689 @@
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+                "input": {
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+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 3246, 
+                "top": 368
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c11,c2\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": []
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+                "input": {
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+                    "output_name": "out_file1"
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+            }, 
+            "inputs": [], 
+            "name": "Tabular-to-FASTA", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 3455, 
+                "top": 458
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "tab2fasta", 
+            "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
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+        }, 
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+                "input": {
+                    "id": 21, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTA Width", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 3653, 
+                "top": 359
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"width\": \"\\\"80\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Mar 17 16:03:12 2014 -0500
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<repositories description="Required tools for proteomics_rnaseq_splice_db_workflow">
+    <repository name="fasta_formatter" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="8f0ae92440b8" />
+    <repository name="rsem" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="59459de65740" />
+</repositories>