Mercurial > repos > jjohnson > cdhit

comparison cd_hit_est.xml @ 1:34a799d173f7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add tool_dependencies and functional test
author Jim Johnson <jj@umn.edu>
date Fri, 07 Sep 2012 13:52:03 -0500
parents 23f5701549b1
children cca0838c1597
comparison
equal deleted inserted replaced
0:23f5701549b1 1:34a799d173f7
1 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.0"> 1 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.1">
2 <description>Cluster a nucleotide dataset into representative sequences</description> 2 <description>Cluster a nucleotide dataset into representative sequences</description>
3 <requirements>
4 <requirement type="package" version="4.6.1">cd-hit</requirement>
5 </requirements>
3 <command> 6 <command>
4 cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand 7 cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand
5 </command> 8 </command>
6 <inputs> 9 <inputs>
7 <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/> 10 <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/>
22 </inputs> 25 </inputs>
23 <outputs> 26 <outputs>
24 <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/> 27 <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
25 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/> 28 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
26 </outputs> 29 </outputs>
27 <requirements>
28 <requirement type="binary">cd-hit-est</requirement>
29 </requirements>
30 <tests> 30 <tests>
31 <test>
32 <param name="fasta_in" value="cd_hit_est_in.fa" />
33 <param name="similarity" value="0.9"/>
34 <param name="wordsize" value="8"/>
35 <output name="clusters_out">
36 <assert_contents>
37 <has_text text=">Cluster" />
38 <has_text_matching expression=">F12Fcsw_481739" />
39 </assert_contents>
40 </output>
41 <output name="fasta_out">
42 <assert_contents>
43 <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
44 </assert_contents>
45 </output>
46 </test>
31 </tests> 47 </tests>
32 <help> 48 <help>
33 **CD-HIT-EST** 49 **CD-HIT-EST**
34 50
35 CD-HIT_ stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database. 51 CD-HIT_ stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.