Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/GeneTrackToWig.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="GeneTrackToWig" name="GeneTrack to Wig" version="1.1.0">
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2 <description>converter</description>
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3 <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="tabular" label="Input GeneTrack index" />
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6 <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" />
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7 <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="wig" metadata_source="input" />
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11 </outputs>
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12 <tests>
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13 <test>
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14 <param name="input" value="test.genetrack" ftype="tabular"/>
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15 <param name="shift" value="73"/>
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16 <param name="zero" value="true"/>
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17 <param name="chromInfo" value="sacCer2"/>
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18 <output name="output" file="geneTrackToWig1.wig"/>
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19 </test>
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20 <test>
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21 <param name="input" value="test.genetrack" ftype="tabular"/>
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22 <param name="shift" value="0"/>
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23 <param name="zero" value="false"/>
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24 <param name="chromInfo" value="sacCer2"/>
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25 <output name="output" file="geneTrackToWig2.wig"/>
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26 </test>
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27 </tests>
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28 <help>
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29
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30 This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them.
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32 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html
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34 .. class:: warningmark
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35
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36 This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
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38 </help>
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39 </tool>