Mercurial > repos > timpalpant > java_genomics_toolkit

comparison galaxy-conf/GeneTrackToWig.xml @ 12:81d5b81fb3c2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents b1952a90d4bf
children eb53be9a09f4
comparison
equal deleted inserted replaced
11:b1952a90d4bf 12:81d5b81fb3c2
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 $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="genetrack" 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="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)" />
7 </inputs> 8 </inputs>
8 <outputs> 9 <outputs>
9 <data name="output" format="wig" metadata_source="input" /> 10 <data name="output" format="wig" metadata_source="input" />
10 </outputs> 11 </outputs>
11 12
12 <help> 13 <help>
14
15 This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them.
16
17 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html
13 18
14 .. class:: warningmark 19 .. class:: warningmark
15 20
16 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. 21 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.
22
17 </help> 23 </help>
18 </tool> 24 </tool>