Testing with <repeat> parameters

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Testing with <repeat> parameters

Peter Cock
Hello all,

Should unit tests with repeat parameters work? If so, how do I give
each repeat group in the XML for the <test>?

Sample tool here:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list

  <inputs>
    <param name="main_lab" size="30" type="text" value="Venn Diagram"
label="Plot title"/>
    <conditional name="universe">
       <param name="type_select" type="select" label="Implicit or
explicit full ID list?">
         <option value="explicit">Explicit</option>
         <option value="implicit">Implicit (use union of sets below)</option>
       </param>
       <when value="explicit">
           <param name="main" type="data" format="tabular,fasta,fastq,sff"
                     label="Full dataset (with all identifiers)"
                     help="Tabular file (uses column one), FASTA,
FASTQ or SFF file."/>
       </when>
       <when value="implicit"/>
    </conditional>
    <repeat name="sets" min="1" max="3" title="Sets">
      <param name="set" type="data" format="tabular,fasta,fastq,sff"
                     label="Members of set"
                     help="Tabular file (uses column one), FASTA,
FASTQ or SFF file."/>
      <param name="lab" size="30" type="text" value="Group"
label="Caption for set"/>
    </repeat>
  </inputs>

The first test attempts to use the repeat "set"/"lab" once - guessing
at how to give repeat parameters in a test:

    <test>
      <param name="type_select" value="explicit"/>
      <param name="main" value="venn_list.tabular" ftype="tabular"/>
      <param name="main_lab" value="Some Proteins"/>
      <param name="set" value="rhodopsin_proteins.fasta"/>
      <param name="lab" value="Rhodopsins"/>
      <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
    </test>

$ ./run_functional_tests.sh -id venn_list
...
python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py
/mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular
"Some Proteins"
/mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta
"Rhodopsins"   /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat
fasta "Group" /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat
...

This seems to have resulted in two <repeat> entries, and so fails.
What I was expecting was:

python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py
/mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular
"Some Proteins"
/mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta
"Rhodopsins"  /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat

Thanks,

Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/