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 > ___________________________________________________________ > 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/ > > </quote> > Quoted from: > http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp465984... > > > _____________________________________ > Sent from http://dev.list.galaxyproject.org > ___________________________________________________________ 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/