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/
