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>
Quoted from:
http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp4659840.html
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