Re: [galaxy-dev] Testing with <repeat> parameters

Oops, I was replying via theGalaxy Development List Archive http://dev.list.galaxyproject.org/ interface, strange it has put the reply off list...

So no functional test for my tool ( despite my enthousiasm :-) ), since the repeat tags must be provided in the test.

Thanks, Joachim.

Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

On 07/16/2013 01:46 PM, Peter Cock wrote:

Off list?

They don't work yet, bar the simplest case of 0 or 1 repeats using a single parameter perhaps.

Peter

On Tuesday, July 16, 2013, wrote:

Hi Peter,

I was wondering if you have details on how to include tests for
repeat tag sets?

Cheers,
Joachim

<quote author='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
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</quote>
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http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp4659840.html


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