Mercurial > repos > timpalpant > java_genomics_toolkit
diff galaxy-conf/IntervalToBed.xml @ 18:b2a69d34385a draft
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
author | timpalpant |
---|---|
date | Fri, 15 Jun 2012 15:07:33 -0400 |
parents | 3e477c7e0e73 |
children |
line wrap: on
line diff
--- a/galaxy-conf/IntervalToBed.xml Sat Jun 09 16:10:42 2012 -0400 +++ b/galaxy-conf/IntervalToBed.xml Fri Jun 15 15:07:33 2012 -0400 @@ -1,15 +1,19 @@ -<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed to Bed" version="1.0.0"> +<tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0"> <description>converter</description> <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command> <inputs> - <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph" label="Input" /> + <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" /> </inputs> <outputs> <data name="output" format="bed" metadata_source="input" /> </outputs> <help> -This tool will convert any file in SAM, BAM, GFF, BedGraph, or BigBed format to Bed format. +This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format. + +.. class:: warningmark + +For SAM/BAM data, paired-end reads are converted to Bed format as the entire fragment (5' end of mate 1 to the 5' end of mate 2). Single-end reads are converted to Bed format as the read itself, with strand information. If your SAM/BAM file contains both mate alignments from a paired-end sequencing run (i.e. two entries for each fragment), you should first filter out reads from either the + or - strand with the SAM Tools -> Filter SAM tool to avoid producing redundant entries in the output Bed file. </help> </tool>