Mercurial > repos > timpalpant > java_genomics_toolkit

annotate 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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b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
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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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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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2 <description>converter</description>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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3 <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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4 <inputs>
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b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
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5 <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" />
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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6 </inputs>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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7 <outputs>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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8 <data name="output" format="bed" metadata_source="input" />
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
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9 </outputs>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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10 <help>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
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12 This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format.
b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents: 15
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b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents: 15
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14 .. class:: warningmark
b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents: 15
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b2a69d34385a Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents: 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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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
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18 </help>
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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19 </tool>