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comparison galaxy-conf/BaseAlignCounts.xml @ 12:81d5b81fb3c2 draft

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Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents 9266d807ca85
children eb53be9a09f4
comparison
equal deleted inserted replaced
11:b1952a90d4bf 12:81d5b81fb3c2
1 <tool id="BaseAlignCounts" name="Map 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 read length)" />
8 <outputs> 8 <outputs>
9 <data name="output" format="wig" /> 9 <data name="output" format="wig" />
10 </outputs> 10 </outputs>
11 11
12 <help> 12 <help>
13 .. class:: warningmark 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 requires sequencing reads in SAM, BAM, or Bed format. 15
16 -----
17
18 .. class:: warningmark
19
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
22 .. class:: infomark
23
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.
25
26 .. class:: infomark
27
28 **TIP:** If you are going to be using reads in SAM format for multiple analyses, it is often more efficient to first convert it into BAM format using NGS: SAM Tools -> SAM-to-BAM.
29
30 -----
31
32 **Syntax**
33
34 - **Sequencing reads** are mapped reads from a high-throughput sequencing experiment.
35 - **In silico extension:** Reads will be artificially extended from their 5' end to be this length.
36
16 </help> 37 </help>
17 </tool> 38 </tool>