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=explicitExplicit/option option value=implicitImplicit (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-tp4659840.html _ 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/
Re: [galaxy-dev] Testing with repeat parameters
OK, it seems that the current state of the functional test framework 'simulates' one click on the 'repeat' button. You just provide one set of param names contained within the repeat block. Luckily, this is enough for my tool now. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:49 PM, Joachim Jacob | VIB | wrote: 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=explicitExplicit/option option value=implicitImplicit (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-tp4659840.html _ 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/ ___ 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
[galaxy-dev] Testing with repeat parameters
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=explicitExplicit/option option value=implicitImplicit (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/
