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
>> ___________________________________________________________
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