Dear Peter, dear John, dear all Thanks very much. This is exactly what I need and the code changes proposed work perfectly as they are. At a short glance even the validators work as intended.
Now for the optional special bonus: Is there a way to define the size of the boxes? The ones I see have 4 lines. Can I make them resizable somehow or define a larger size? (size="10" or resize="true" does not seem to do the trick.) Not a very pressing issue though. @Joachim: I am using the same approach elsewhere, but the difference is that it runs a tool multiple times, instead of running it once on multiple inputs. But thanks anyway. Cheers Ulf On 01/10/13 14:08, John Chilton wrote: > Thanks Peter, > > Yeah, looking over unified_genotyper.xml, you would probably just > want to replace: > > #for $i, $input_bam in enumerate( $reference_source.input_bams ): > -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" > "gatk_input_${i}" > #if str( $input_bam.input_bam.metadata.bam_index ) != "None": > -d "" "${input_bam.input_bam.metadata.bam_index}" > "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index > #end if > #end for > > with > > #for $i, $input_bam in enumerate( $reference_source.input_bams ): > -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}" > #if str( $input_bam.metadata.bam_index ) != "None": > -d "" "${input_bam.metadata.bam_index}" "bam_index" > "gatk_input_${i}" ##hardcode galaxy ext type as bam_index > #end if > #end for > > And: > > <repeat name="input_bams" title="BAM file" min="1" > help="-I,--input_file &lt;input_file&gt;"> > <param name="input_bam" type="data" format="bam" label="BAM > file"> > <validator type="unspecified_build" /> > <validator type="dataset_metadata_in_data_table" > table_name="gatk_picard_indexes" metadata_name="dbkey" > metadata_column="dbkey" message="Sequences are not currently available > for the specified build." /> <!-- fixme!!! this needs to be a select > --> > </param> > </repeat> > > with > > <param name="input_bams" type="data" multiple="true" > format="bam" label="BAM file"> > <validator type="unspecified_build" /> > <validator type="dataset_metadata_in_data_table" > table_name="gatk_picard_indexes" metadata_name="dbkey" > metadata_column="dbkey" message="Sequences are not currently available > for the specified build." /> <!-- fixme!!! this needs to be a select > --> > </param> > > > And: > > <repeat name="input_bams" title="BAM file" min="1" > help="-I,--input_file &lt;input_file&gt;"> > <param name="input_bam" type="data" format="bam" label="BAM > file" > > </param> > </repeat> > > with > > <param name="input_bams" multiple="true" type="data" > format="bam" label="BAM file" > > </param> > > I have not tested these specific changes, so your millage may vary. I > have no clue if those validators in that second block are going to > work with multiple="true". If you test it out and there is some > problem, please let me know I can try to fix it. > > I don't know if the Galaxy team wants to start replacing these blocks > in its tools - this change would break existing workflows built on the > unified genotyper and I am not sure the Galaxy team has any interest > in using these kind of data blocks going forward. They are working out > great for us on Galaxy-P though. > > -John > > > On Tue, Oct 1, 2013 at 7:57 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> On Tue, Oct 1, 2013 at 1:27 PM, Ulf Schaefer <ulf.schae...@phe.gov.uk> wrote: >>> Dear all >>> >>> We frequently find ourselves in situations where a tool needs to be run >>> with a lot of input files. For example, run the GATK UnifiedGenotyper >>> with easily dozens of bam files. >>> >>> Using the <repeat> in this case requires quite a bit of clicking. Is >>> there a more conventient way fo doing this? Maybe similar to the >>> multi-file-select that is possible for workflow inputs? >>> >>> I saw some older discussions on this or similar issues, but I am a bit >>> lost what the current official stable proposed solution for this is. >>> >>> Thanks for your help >>> Ulf >> >> Use <param type="data" multiple="true" ... > instead of using >> <repeat ...><param type="data" ...></repeat>. >> >> I asked John Chilton about this recently via Twitter, and it is >> now on the wiki, >> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax >> >> Simple example here: >> https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant/src/tip/iquant.xml?at=default >> >> Peter >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. 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