Mercurial > repos > timpalpant > java_genomics_toolkit
diff galaxy-conf/GeneTrackToWig.xml @ 20:9d56b5b85740 draft
Reuploaded to see if tools get loaded correctly this time.
author | timpalpant |
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date | Fri, 15 Jun 2012 15:10:26 -0400 |
parents | |
children | b43c420a6135 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/GeneTrackToWig.xml Fri Jun 15 15:10:26 2012 -0400 @@ -0,0 +1,39 @@ +<tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.1.0"> + <description>converter</description> + <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command> + <inputs> + <param name="input" type="data" format="tabular" label="Input GeneTrack index" /> + <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" /> + <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" /> + </inputs> + <outputs> + <data name="output" format="wig" metadata_source="input" /> + </outputs> + <tests> + <test> + <param name="input" value="test.genetrack" ftype="tabular"/> + <param name="shift" value="73"/> + <param name="zero" value="true"/> + <param name="chromInfo" value="sacCer2"/> + <output name="output" file="geneTrackToWig1.wig"/> + </test> + <test> + <param name="input" value="test.genetrack" ftype="tabular"/> + <param name="shift" value="0"/> + <param name="zero" value="false"/> + <param name="chromInfo" value="sacCer2"/> + <output name="output" file="geneTrackToWig2.wig"/> + </test> + </tests> +<help> + +This tool will convert GeneTrack_ format files into Wig files, optionally offsetting the + and - strand counts by a specified value before merging them. + +.. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html + +.. class:: warningmark + +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. + +</help> +</tool>