Mercurial > repos > bgruening > eden_cluster_motif_finder
view motif_finder.xml @ 0:95a776023fbc draft
Uploaded
author | bgruening |
---|---|
date | Thu, 12 Jun 2014 11:35:21 -0400 |
parents | |
children | f8111c9f037d |
line wrap: on
line source
<tool id="eden_cluster_motif_finder" name="Motif finder" version="0.1.0"> <description>based on EDeN</description> <requirements> <requirement type="package" version="1.6.1">biopython</requirement> <requirement type="package" version="13.5">eden</requirement> </requirements> <command interpreter="python"> eden_cluster_motif_finder.py --input-file $infile --radius $radius --distance $distance --output-dir ./ --num-nearest-neighbors $num_nearest_neighbors --neighborhood-intersection-size $neighborhood_intersection_size --fraction-center-scan $fraction_center_scan --output-file foo.txt --max-order $max_order --min-motif-size $min_motif_size --num-negative-repetitions $num_negative_repetitions > $output </command> <inputs> <param name="infile" type="data" format="fasta" label="sequences" help="in FASTA format (--input-file)"/> <param name="radius" type="integer" value="2" label="Size of the largest radius used in EDeN" help="(--radius)" /> <param name="distance" type="integer" value="5" label="Size of the largest distance used in EDeN" help="(--distance)" /> <param name="num_nearest_neighbors" type="integer" value="10" label="Number of nearest neighbors used in the density estimation" help="(--num-nearest-neighbors)" /> <param name="neighborhood_intersection_size" type="integer" value="5" label="Number of nearest neighbors that must be shared in neighborhood in order to trigger neighborhood joining." help="(--neighborhood-intersection-size)" /> <param name="fraction_center_scan" type="float" value="1.0" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" /> <param name="max_order" type="integer" value="3" label="Size of the order for negative shuffling" help="(--max_order)" /> <param name="min_motif_size" type="integer" value="4" label="Size of the smallest returned motif" help="(--min-motif-size)" /> <param name="num_negative_repetitions" type="integer" value="3" label="Size of the smallest returned motif" help="(--num-negative-repetitions)" /> </inputs> <outputs> <data format="tabular" name="output" label="${tool.name} on ${on_string}"/> </outputs> <tests> </tests> <help> **What it does** EDeN Motif finder ----- **Parameters** **References** Fabrizio Costa </help> </tool>