comparison cd_hit_est.xml @ 6:f0c20796d33a

Update tool_dependencies, reinstate test

5:22b6a4412ea6

 <outputs>
  <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
 </outputs>
 <tests>
  <!--
  <test>
    <param name="fasta_in" value="cd_hit_est_in.fa" />
    <param name="similarity" value="0.9"/>
    <param name="wordsize" value="8"/>
    <output name="clusters_out">

        <assert_contents>
            <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
        </assert_contents>
    </output>
  </test>
  -->
 </tests>
 <help>
**CD-HIT-EST**

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.

6:f0c20796d33a

 <outputs>
  <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
 </outputs>
 <tests>
  <test>
    <param name="fasta_in" value="cd_hit_est_in.fa" />
    <param name="similarity" value="0.9"/>
    <param name="wordsize" value="8"/>
    <output name="clusters_out">

        <assert_contents>
            <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
        </assert_contents>
    </output>
  </test>
 </tests>
 <help>
**CD-HIT-EST**

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.