Mercurial > repos > bgruening > eden_cluster_motif_finder
comparison motif_finder.xml @ 2:295e085b8d60 draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 12 Jun 2014 12:22:56 -0400 |
| parents | f8111c9f037d |
| children |
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| 1:f8111c9f037d | 2:295e085b8d60 |
|---|---|
| 1 <tool id="eden_cluster_motif_finder" name="Motif finder" version="0.1.0"> | 1 <tool id="eden_cluster_motif_finder" name="Motif finder" version="0.1.0"> |
| 2 <description>based on EDeN</description> | 2 <description>based on EDeN</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.63">biopython</requirement> | 4 <requirement type="package" version="1.63">biopython</requirement> |
| 5 <requirement type="package" version="1.3.5">eden</requirement> | 5 <requirement type="package" version="10">eden</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command interpreter="python"> | 7 <command interpreter="python"> |
| 8 eden_cluster_motif_finder.py | 8 eden_cluster_motif_finder.py |
| 9 | 9 |
| 10 --input-file $infile | 10 --input-file $infile |
| 11 --radius $radius | 11 --radius $radius |
| 12 --distance $distance | 12 --distance $distance |
| 13 --output-dir ./ | 13 --output-dir "./foo" |
| 14 --num-nearest-neighbors $num_nearest_neighbors | 14 --num-nearest-neighbors $num_nearest_neighbors |
| 15 --neighborhood-intersection-size $neighborhood_intersection_size | 15 --neighborhood-intersection-size $neighborhood_intersection_size |
| 16 --fraction-center-scan $fraction_center_scan | 16 --fraction-center-scan $fraction_center_scan |
| 17 --output-file foo.txt | 17 --output-file foo.txt |
| 18 --max-order $max_order | 18 --max-order $max_order |
| 19 --min-motif-size $min_motif_size | 19 --min-motif-size $min_motif_size |
| 20 --num-negative-repetitions $num_negative_repetitions | 20 --num-negative-repetitions $num_negative_repetitions |
| 21 > $output | 21 --motif-file $output |
| 22 </command> | 22 </command> |
| 23 <inputs> | 23 <inputs> |
| 24 <param name="infile" type="data" format="fasta" label="sequences" help="in FASTA format (--input-file)"/> | 24 <param name="infile" type="data" format="fasta" label="sequences" help="in FASTA format (--input-file)"/> |
| 25 <param name="radius" type="integer" value="2" label="Size of the largest radius used in EDeN" help="(--radius)" /> | 25 <param name="radius" type="integer" value="2" label="Size of the largest radius used in EDeN" help="(--radius)" /> |
| 26 <param name="distance" type="integer" value="5" label="Size of the largest distance used in EDeN" help="(--distance)" /> | 26 <param name="distance" type="integer" value="5" label="Size of the largest distance used in EDeN" help="(--distance)" /> |
| 27 <param name="num_nearest_neighbors" type="integer" value="10" label="Number of nearest neighbors used in the density estimation" help="(--num-nearest-neighbors)" /> | 27 <param name="num_nearest_neighbors" type="integer" value="10" label="Number of nearest neighbors used in the density estimation" help="(--num-nearest-neighbors)" /> |
| 28 <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." | 28 <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." |
| 29 help="(--neighborhood-intersection-size)" /> | 29 help="(--neighborhood-intersection-size)" /> |
| 30 <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)" /> | 30 <param name="fraction_center_scan" type="integer" value="1" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" /> |
| 31 <param name="max_order" type="integer" value="3" label="Size of the order for negative shuffling" help="(--max_order)" /> | 31 <param name="max_order" type="integer" value="3" label="Size of the order for negative shuffling" help="(--max_order)" /> |
| 32 <param name="min_motif_size" type="integer" value="4" label="Size of the smallest returned motif" help="(--min-motif-size)" /> | 32 <param name="min_motif_size" type="integer" value="4" label="Size of the smallest returned motif" help="(--min-motif-size)" /> |
| 33 <param name="num_negative_repetitions" type="integer" value="3" label="Size of the smallest returned motif" help="(--num-negative-repetitions)" /> | 33 <param name="num_negative_repetitions" type="integer" value="3" label="Size of the smallest returned motif" help="(--num-negative-repetitions)" /> |
| 34 </inputs> | 34 </inputs> |
| 35 <outputs> | 35 <outputs> |