Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/IntervalToBed.xml @ 18:b2a69d34385a draft
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
author | timpalpant |
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date | Fri, 15 Jun 2012 15:07:33 -0400 |
parents | 3e477c7e0e73 |
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rev | line source |
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b2a69d34385a
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents:
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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.
timpalpant
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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.
timpalpant
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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.
timpalpant
parents:
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4 <inputs> |
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b2a69d34385a
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents:
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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.
timpalpant
parents:
diff
changeset
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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.
timpalpant
parents:
diff
changeset
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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.
timpalpant
parents:
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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
parents:
diff
changeset
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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.
timpalpant
parents:
diff
changeset
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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.
timpalpant
parents:
diff
changeset
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11 |
18
b2a69d34385a
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents:
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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
diff
changeset
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13 |
b2a69d34385a
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents:
15
diff
changeset
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14 .. class:: warningmark |
b2a69d34385a
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents:
15
diff
changeset
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15 |
b2a69d34385a
Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.
timpalpant
parents:
15
diff
changeset
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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.
timpalpant
parents:
diff
changeset
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17 |
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
parents:
diff
changeset
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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.
timpalpant
parents:
diff
changeset
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19 </tool> |