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comparison galaxy-conf/GeneTrackToWig.xml @ 13:eb53be9a09f4 draft

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author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children 3e477c7e0e73
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12:81d5b81fb3c2 13:eb53be9a09f4
1 <tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.0.0"> 1 <tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.0.0">
2 <description>converter</description> 2 <description>converter</description>
3 <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
4 <inputs> 4 <inputs>
5 <param name="input" type="data" format="genetrack" label="Input GeneTrack index" /> 5 <param name="input" type="data" format="tabular" label="Input GeneTrack index" />
6 <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" /> 6 <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" />
7 <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" /> 7 <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
8 </inputs> 8 </inputs>
9 <outputs> 9 <outputs>
10 <data name="output" format="wig" metadata_source="input" /> 10 <data name="output" format="wig" metadata_source="input" />
11 </outputs> 11 </outputs>
12 12 <tests>
13 <test>
14 <param name="input" value="test.genetrack" ftype="tabular"/>
15 <param name="shift" value="73"/>
16 <param name="zero" value="true"/>
17 <param name="chromInfo" value="sacCer2"/>
18 <output name="output" file="geneTrackToWig1.wig"/>
19 </test>
20 <test>
21 <param name="input" value="test.genetrack" ftype="tabular"/>
22 <param name="shift" value="0"/>
23 <param name="zero" value="false"/>
24 <param name="chromInfo" value="sacCer2"/>
25 <output name="output" file="geneTrackToWig2.wig"/>
26 </test>
27 </tests>
13 <help> 28 <help>
14 29
15 This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them. 30 This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them.
16 31
17 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html 32 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html