Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/IntervalToBed.xml @ 20:9d56b5b85740 draft
Reuploaded to see if tools get loaded correctly this time.
| author | timpalpant |
|---|---|
| date | Fri, 15 Jun 2012 15:10:26 -0400 |
| parents | |
| children | b43c420a6135 |
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| 19:8ad390e82b92 | 20:9d56b5b85740 |
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| 1 <tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0"> | |
| 2 <description>converter</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" /> | |
| 6 </inputs> | |
| 7 <outputs> | |
| 8 <data name="output" format="bed" metadata_source="input" /> | |
| 9 </outputs> | |
| 10 <help> | |
| 11 | |
| 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. | |
| 17 | |
| 18 </help> | |
| 19 </tool> |