On Tue, Mar 11, 2014 at 2:58 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Peter,
I think you need to have:
<change_format> <when input="output.out_format" value="0" format="txt"/> <when input="output.out_format" value="0 -html" format="html"/> <when input="output.out_format" value="2" format="txt"/> <when input="output.out_format" value="2 -html" format="html"/> <when input="output.out_format" value="4" format="txt"/> <when input="output.out_format" value="4 -html" format="html"/> <when input="output.out_format" value="5" format="blastxml"/> </change_format>
Sorry, can't test it right now.
That seems to work - thanks Björn :) This seems to have exposed a bug in the <test> framework, e.g. <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="database" value="" /> <param name="evalue_cutoff" value="1e-40" /> <param name="out_format" value="5" /> <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> </test> This was saying the output should have been "blastxml", but until I just fixed it the output was being tagged as "tabular" (although run_functional_tests.sh did check the content it didn't check the datatype matched). Dave - do think this is a reasonable enhancement? Peter