Mercurial > repos > nikos > ucsc_tools
changeset 6:558f7f9baa78 draft
Uploaded
| author | nikos |
|---|---|
| date | Tue, 15 Jul 2014 07:19:46 -0400 |
| parents | 998c98233c36 |
| children | eebdd6da9353 |
| files | make_ucsc_track.xml |
| diffstat | 1 files changed, 34 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_ucsc_track.xml Tue Jul 15 07:19:46 2014 -0400 @@ -0,0 +1,34 @@ +<tool id="make_ucsc_track" name="UCSC Track Line"> + <description> Create a track line to import a bigWig or bigBed file in the UCSC genome browser </description> + <command interpreter="bash"> + make_ucsc_track.sh -i $input -t ${input.ext} -n '$name' -o $assembly > $output + </command> + <inputs> + <param name="input" type="data" format="bigwig,bigbed" label="Input file" help="bigWig or bigBEd format." /> + <param name="name" type="text" label="Track name" help="Type the track name you want to appear when you import the file in the UCSC browser." > + <validator type="empty_field" /> + </param> + + <param name="assembly" type="text" label="Orgamism assembly" help="E.g. hg19" > + <validator type="empty_field" /> + </param> + +<!-- <param name="visibility" type="select" label="Track visibility"> + <option value="3">Full</option> + <option value="2">Pack</option> + <option value="1">Dense</option> + </param> +--> + </inputs> + + <outputs> + <data format="txt" name="output"/> + </outputs> + <help> +This tool creates a UCSC track line for a bigWig or bigBed dataset in Galaxy. The text output can be pasted in the "Paste URLs or data" form in the `Add Custom Tracks`_ section of the UCSC Genome Browser. + +.. _Add Custom Tracks: http://genome.ucsc.edu/cgi-bin/hgCustom + + </help> +</tool> +