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comparison galaxy-conf/IntervalLengthDistribution.xml @ 24:a77e126ae856 draft

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Reupload since last upload did not load correctly
author timpalpant
date Tue, 19 Jun 2012 22:15:09 -0400
parents 9d56b5b85740
children b43c420a6135
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23:01d5d20eaadd 24:a77e126ae856
1 <tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0">
2 <description>of read lengths</description>
3 <command interpreter="sh">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
4 <inputs>
5 <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" />
6 <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
7 </inputs>
8 <outputs>
9 <data format="tabular" name="output" />
10 </outputs>
11 <tests>
12 <test>
13 <param name="input" value="test.bed"/>
14 <param name="freq" value="false"/>
15 <output name="output" file="intervallengthdistribution1.txt"/>
16 </test>
17 <test>
18 <param name="input" value="test.bed"/>
19 <param name="freq" value="true"/>
20 <output name="output" file="intervallengthdistribution2.txt"/>
21 </test>
22 <test>
23 <param name="input" value="test2.bed"/>
24 <param name="freq" value="false"/>
25 <output name="output" file="intervallengthdistribution3.txt"/>
26 </test>
27 </tests>
28
29 <help>
30
31 This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format.
32
33 .. class:: warningmark
34
35 For paired-end sequencing reads, the length is the length of the fragment (5' end of read 1 to 5' end of read 2)
36
37 </help>
38 </tool>