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comparison galaxy-conf/IntervalToBed.xml @ 18:b2a69d34385a draft

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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
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17:ace7855c1017 18:b2a69d34385a
1 <tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed to Bed" version="1.0.0"> 1 <tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0">
2 <description>converter</description> 2 <description>converter</description>
3 <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
4 <inputs> 4 <inputs>
5 <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph" label="Input" /> 5 <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" />
6 </inputs> 6 </inputs>
7 <outputs> 7 <outputs>
8 <data name="output" format="bed" metadata_source="input" /> 8 <data name="output" format="bed" metadata_source="input" />
9 </outputs> 9 </outputs>
10 <help> 10 <help>
11 11
12 This tool will convert any file in SAM, BAM, GFF, BedGraph, or BigBed format to Bed format. 12 This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format.
13
14 .. class:: warningmark
15
16 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.
13 17
14 </help> 18 </help>
15 </tool> 19 </tool>