Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/MapDyads.xml @ 22:727fbba02ef7 draft

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Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.
author timpalpant
date Tue, 19 Jun 2012 22:09:23 -0400
parents 9d56b5b85740
children b43c420a6135
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1 <tool id="MapDyads" name="Map dyads" version="1.1.0">
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2 <description>from sequencing reads</description>
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3 <command interpreter="sh">
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4 galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output
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5 #if $type.read == 'single'
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6 -s $type.size
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7 #end if
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8 </command>
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9 <inputs>
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10 <param name="input" type="data" format="sam,bam,bed,bedGraph" label="Sequencing reads" />
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11 <conditional name="type">
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12 <param name="read" type="select" label="Type of reads">
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13 <option value="paired" selected="true">Paired-End</option>
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14 <option value="single">Single-End</option>
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15 </param>
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16 <when value="single">
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17 <param name="size" type="integer" value="147" label="Estimated mononucleosome length (used to offset +/- strands)" />
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18 </when>
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19 <when value="paired">
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20 <!-- No values here -->
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21 </when>
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22 </conditional>
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="wig" />
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26 </outputs>
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27
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28 <help>
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29
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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.
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31
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32 .. class:: warningmark
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33
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34 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format.
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36 .. class:: warningmark
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38 Since BedGraph format does not contain strand information, all reads in BedGraph format are considered to be on the 5' strand.
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39
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40 </help>
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41 </tool>