Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalToBed.xml @ 20:9d56b5b85740 draft

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Reuploaded to see if tools get loaded correctly this time.
author timpalpant
date Fri, 15 Jun 2012 15:10:26 -0400
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children b43c420a6135
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1 <tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0">
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2 <description>converter</description>
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3 <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" />
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6 </inputs>
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7 <outputs>
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8 <data name="output" format="bed" metadata_source="input" />
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9 </outputs>
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10 <help>
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11
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12 This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format.
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13
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14 .. class:: warningmark
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15
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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.
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17
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18 </help>
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19 </tool>