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comparison galaxy-conf/MapDyads.xml @ 20:9d56b5b85740 draft

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Reuploaded to see if tools get loaded correctly this time.
author timpalpant
date Fri, 15 Jun 2012 15:10:26 -0400
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children b43c420a6135
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19:8ad390e82b92 20:9d56b5b85740
1 <tool id="MapDyads" name="Map dyads" version="1.1.0">
2 <description>from sequencing reads</description>
3 <command interpreter="sh">
4 galaxyToolRunner.sh nucleosomes.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="sam,bam,bed,bedGraph" 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
30 This tool produces a Wig file with the number of dyads at each base pair. For paired-end MNase data, dyads are approximated using the center of the fragment. For Bed/BedGraph formatted input, this means the center of the interval; for SAM/BAM formatted input, this means the middle between the 5' end of mate 1 and the 5' end of mate 2. For single-end data, the estimated mononucleosome fragment length (N) must be specified, which will be used to offset reads from the + and - strands by +/- N/2.
31
32 .. class:: warningmark
33
34 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format.
35
36 .. class:: warningmark
37
38 Since BedGraph format does not contain strand information, all reads in BedGraph format are considered to be on the 5' strand.
39
40 </help>
41 </tool>