# 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 @@ + + + + + +