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comparison galaxy-conf/MapDyads.xml @ 4:4b32ed5d4a1b

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author timpalpant
date Tue, 14 Feb 2012 00:59:33 -0500
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3:4b610dc8f6ba 4:4b32ed5d4a1b
1 <tool id="MapDyads" name="Map dyads" version="1.0.0">
2 <description>from sequencing reads</description>
3 <command interpreter="sh">
4 galaxyToolRunner.sh nucleosome.MapDyads -i $input -a ${chromInfo} -o $output
5 #if $type.read == 'single'
6 -s $type.size
7 #end if
8 </command>
9 <inputs>
10 <param name="input" type="data" format="bam" label="Sequencing reads" />
11 <conditional name="type">
12 <param name="read" type="select" label="Type of reads">
13 <option value="paired" selected="true">Paired-End</option>
14 <option value="single">Single-End</option>
15 </param>
16 <when value="single">
17 <param name="size" type="integer" value="147" label="Estimated mononucleosome length (used to offset +/- strands)" />
18 </when>
19 <when value="paired">
20 <!-- No values here -->
21 </when>
22 </conditional>
23 </inputs>
24 <outputs>
25 <data name="output" format="wig" />
26 </outputs>
27
28 <help>
29 .. class:: warningmark
30
31 This tool requires sequencing reads in BAM format. If your reads are in SAM format, use the SAM-to-BAM tool under NGS: SAMTools.
32
33 .. class:: warningmark
34
35 For paired-end MNase data, read centers are approximated by using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands.
36 </help>
37 </tool>