Mercurial > repos > jjohnson > cdhit
comparison cd_hit_est.xml @ 2:cca0838c1597
Add an environment variable for the -M and -T options for memory and thread allocation
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 26 Feb 2013 12:11:36 -0600 |
| parents | 34a799d173f7 |
| children | 43724ea1c85f |
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| 1:34a799d173f7 | 2:cca0838c1597 |
|---|---|
| 1 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.1"> | 1 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.2"> |
| 2 <description>Cluster a nucleotide dataset into representative sequences</description> | 2 <description>Cluster a nucleotide dataset into representative sequences</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="4.6.1">cd-hit</requirement> | 4 <requirement type="package" version="4.6.1">cd-hit</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command> | 6 <command> |
| 7 cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand | 7 cd-hit-est \$CDHIT_SITE_OPTIONS -i "$fasta_in" -o rep_seq -c $similarity -n $wordsize $strand |
| 8 </command> | 8 </command> |
| 9 <inputs> | 9 <inputs> |
| 10 <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/> | 10 <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/> |
| 11 <param name="similarity" type="float" value="0.9" label="similarity threshold: .75 - 1.0, default is .9"> | 11 <param name="similarity" type="float" value="0.9" label="similarity threshold: .75 - 1.0, default is .9"> |
| 12 <validator type="in_range" message="sequence similarity threshold should be .75 - 1.0" min=".75" max="1.0"/> | 12 <validator type="in_range" message="sequence similarity threshold should be .75 - 1.0" min=".75" max="1.0"/> |