Mercurial > repos > alermine > nebula
view [APliBio]Nebula tools suite/Nebula/MotifDiscovery/chipmunk.xml @ 1:0ec82f1785af draft
Uploaded
author | alermine |
---|---|
date | Wed, 14 Nov 2012 05:59:25 -0500 |
parents | 2ec3ba0e9e70 |
children |
line wrap: on
line source
<tool id="chipmunk_chiphorde" name="ChIPmunk" version="1.0.0"> <description>De novo motif finding</description> <command interpreter="bash">chipmunk.sh -f $inputfile -n $motif_number_selector -m $minw -v $maxw -z $mode -o $log_outfile -p $processed_output -i $image_output -x "$name" -y ${GALAXY_DATA_INDEX_DIR}</command> <inputs> <param name="name" type="text" value="ChIPseq" label="Name" /> <param format="fasta" name="inputfile" type="data" label="Sequences"/> <param name="motif_number_selector" type="select" label="Number of different motifs to search"> <option value="1">1</option> <option value="2">2</option> <option value="3" selected="true">3</option> <option value="4">4</option> </param> <param name="minw" type="integer" value="10" label="Min width of motif to search" /> <param name="maxw" type="integer" value="15" label="Max width of motif to search" /> <param name="mode" type="select" label="Mode for additional motif finding" help="use 'mask' to mask already identified motifs in your sequences and 'filter' to filter out the whole sequences with already identified motifs"> <option value="filter">filter</option> <option value="mask" selected="true">mask</option> </param> </inputs> <outputs> <data format="log" name="log_outfile" label="row ChIPmunk output for ${name} (log)"/> <data format="txt" name="processed_output" label="motifs for ${name}(txt)"/> <data format="png" name="image_output" label="motifs for ${name}(png)"/> </outputs> <help> **What it does** ChIPmunk detects over-represented non-overlapping motifs in fasta sequences </help> </tool>