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annotate galaxy-conf/MapDyads.xml @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents 81d5b81fb3c2
children
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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32 .. class:: warningmark
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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.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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39
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40 </help>
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41 </tool>