review changes

tools/rna_tools/cmsearch_deoverlap/cmsearch-deoverlap.xml

@@ -20,10 +20,10 @@
 
  ]]></command>
  <inputs>
- <param type="data" name="clan_information" format="txt" label="clan information" help="Each row in the file contains an RNA clan and its corresponding family members"/>
- <param type="data" name="cmsearch_matches" format="tabular" label="cmsearch tabular format results (--tblout)"/>
+ <param type="data" name="clan_information" format="txt" label="clan information" help="Each row in the file contains a RNA clan and its corresponding family members"/>
+ <param type="data" name="cmsearch_matches" format="tabular" label="cmsearch tabular format result (--tblout)"/>
  <param argument="--maxkeep" type="boolean" truevalue="--maxkeep" falsevalue="" label="keep hits that only overlap with other hits that are not kept [default: remove all hits with higher scoring overlap]" />
- <param name="dirty" type="boolean" truevalue="--dirty" falsevalue="" label="keep intermediate files (sorted tblout files)" help="(--dirty)"/>
+ <param name="dirty" type="boolean" truevalue="--dirty" falsevalue="" label="keep intermediate file (sorted tblout file)" help="(--dirty)"/>
  </inputs>
  <outputs>
  <data name="deoverlapped_matches" format="tabular" label="Deoverlapped matches" />
@@ -32,14 +32,14 @@
  </data>
  </outputs>
  <tests>
- <test>
+ <test expect_num_outputs="2">
  <param name="clan_information" value="ribo.claninfo" />
  <param name="cmsearch_matches" value="1.cmsearch.tblout" />
  <param name="dirty" value="--dirty"/>
  <output name="deoverlapped_matches" file="1.cmsearch.tblout.deoverlapped" />
  <output name="matches_sort" file="1.cmsearch.tblout.sort" />
  </test>
- <test>
+ <test expect_num_outputs="1">
  <param name="clan_information" value="ribo.claninfo" />
  <param name="cmsearch_matches" value="1.cmsearch.tblout" />
  <param name="dirty" value=""/>