Hi Nicola,
Thanks for the response, I'm still getting the same issue though. I've followed the set up you've shown for bowtie_wrappers but am getting the same error. I've changed my file structure to look like this:
tmp/test.xml:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
tmp/tool_data_table_conf.xml.sample:
<tables> <table name="twobit_indexes" comment_char="#"> <columns>value, path</columns> <file path="tool-data/twobit.loc" /> </table> </tables>
tmp/tool_data_table_conf.xml.test:
<tables> <!-- Locations of indexes in the 2bit format --> <table name="twobit" comment_char="#" allow_duplicate_entries="False"> <columns>value, path</columns> <file path="${__HERE__}/test-data/twobit.loc" /> </table> </tables>
tmp/tool-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
tmp/tool-data/twobit.loc
#
tmp/test-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Rather than placing these twobit.loc files etc... under tmp with test.xml I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either.
I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated.
Thanks!
On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:
Hi D K, for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_ wrappers
Your tool_data_table_conf.xml.test should be different from your .sample and contain:
<file path="${__HERE__}/test-data/twobit.loc" />
Please note the use of ${__HERE__} to indicate the directory where the tool is. You should also have a comment-only tool-data/twobit.loc.sample , while the loc file for testing should be in test-data/twobit.loc
Cheers, Nicola
On 06/10/16 23:08, D K wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test"
(mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries=" False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/ reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
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