# HG changeset patch
# User chrisw
# Date 1549997512 18000
# Node ID d2d9937d1f9c03a51be7b064d2592b22111c7abb
# Parent ae546ad6f2f45130cbbbc62ac0fb1f0aec0c1a60
Uploaded
diff -r ae546ad6f2f4 -r d2d9937d1f9c .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Tue Feb 12 13:51:52 2019 -0500
@@ -0,0 +1,10 @@
+categories:
+ - RNA
+description: Monorail is a RNA-seq analysis which produces coverage & junction summaries
+long_description: |
+ Monorail is a RNA-seq analysis pipeline which produces summarized coverage and junction information w/o the cost of keeping BAMs.
+ It runs STAR, samtools, and bamcount at its core to produce its results efficiently.
+name: monorail
+owner: ChristopherWilks
+remote_repository_url: https://github.com/ChristopherWilks/monorail_galaxy
+type: unrestricted
diff -r ae546ad6f2f4 -r d2d9937d1f9c monorail.sh
--- a/monorail.sh Tue Feb 12 11:56:25 2019 -0500
+++ b/monorail.sh Tue Feb 12 13:51:52 2019 -0500
@@ -29,4 +29,4 @@
samtools index -@ $threads $sorted_bam >> stools.log 2>&1
#get coverage summaries
-bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1
+bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --alts bc > bc.log 2>&1
diff -r ae546ad6f2f4 -r d2d9937d1f9c monorail.xml
--- a/monorail.xml Tue Feb 12 11:56:25 2019 -0500
+++ b/monorail.xml Tue Feb 12 13:51:52 2019 -0500
@@ -2,6 +2,7 @@
samtools
star
+ bamcount
diff -r ae546ad6f2f4 -r d2d9937d1f9c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Feb 12 13:51:52 2019 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+