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comparison galaxy-conf/BaseAlignCounts.xml @ 13:eb53be9a09f4 draft

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author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children 3e477c7e0e73
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12:81d5b81fb3c2 13:eb53be9a09f4
1 <tool id="BaseAlignCounts" name="Calculate coverage" version="1.0.0"> 1 <tool id="BaseAlignCounts" name="Calculate coverage" version="1.0.0">
2 <description>of sequencing reads</description> 2 <description>of sequencing reads</description>
3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
4 <inputs> 4 <inputs>
5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" /> 5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for read length)" /> 6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for fragment length)" />
7 </inputs> 7 </inputs>
8 <outputs> 8 <outputs>
9 <data name="output" format="wig" /> 9 <data name="output" format="wig" />
10 </outputs> 10 </outputs>
11 11 <tests>
12 </tests>
12 <help> 13 <help>
13 14
14 This tool produces a new Wig file with the number of reads/intervals overlapping each base pair. Reads can be artificially extended to match known fragment lengths. If you wish to count the number of reads starting at each base pair, set the read extension to 1. If you wish to count the number of intervals overlapping each base pair, set the extension to -1. 15 This tool produces a new Wig file with the number of reads/intervals overlapping each base pair. Reads can be artificially extended to match known fragment lengths. If you wish to count the number of reads starting at each base pair, set the read extension to 1. If you wish to count the number of intervals overlapping each base pair, set the extension to -1.
15 16
16 ----- 17 -----
17 18
18 .. class:: warningmark 19 .. class:: warningmark
19 20
20 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format. If you are artificially extending reads, ensure that the strand is set correctly in SAM, BAM, and Bed files. 21 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format. If you are artificially extending reads, ensure that the strand is set correctly in SAM, BAM, and Bed files.
22
23 .. class:: warningmark
24
25 Paired-end reads are considered to be the entire fragment (the distance from the 5' end of mate 1 to the 5' end of mate 2) if the extension is set to -1.
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22 .. class:: infomark 27 .. class:: infomark
23 28
24 If you would like to convert valued interval data (e.g. BedGraph files from microarrays) to Wig format, use the Converters -> Interval to Wig converter. 29 If you would like to convert valued interval data (e.g. BedGraph files from microarrays) to Wig format, use the Converters -> Interval to Wig converter.
25 30