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4
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1 <tool id="MapDyads" name="Map dyads" version="1.0.0">
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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 nucleosome.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="bam" 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 .. class:: warningmark
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30
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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.
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32
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33 .. class:: warningmark
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34
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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.
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36 </help>
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37 </tool>
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