Fun question! I have opened a pull request with my answer -
https://bitbucket.org/galaxy/galaxy-central/pull-request/457/allow-cheetah-tool-templates-to-reason/diff.

There are three different hacks you can use right now... here is a
diff against tools/filters/catWrapper.xml I was using the to test them
- all of them require more about the internals of Galaxy then I really
think should be exposed to the tool (or tool author).

diff --git a/tools/filters/catWrapper.xml b/tools/filters/catWrapper.xml
index ec52ba8..060362b 100644
--- a/tools/filters/catWrapper.xml
+++ b/tools/filters/catWrapper.xml
@@ -7,6 +7,11 @@
         #for $q in $queries
             ${q.input2}
         #end for
+        #import galaxy.datatypes.sequence
+        ; echo "${isinstance($input1.datatype,
galaxy.datatypes.sequence.Fastq )}"
+        ; echo
"$input1.datatype.matches_any([galaxy.datatypes.sequence.Fastq])"
+        ; echo "$input1.datatype.matches_any([
$__app__.datatypes_registry.get_datatype_by_extension( 'fastq' )])"
+        ; echo "$input1.is_of_type( 'fastq' )" <!-- Doesn't work yet -->
     </command>
     <inputs>
         <param name="input1" type="data" label="Concatenate Dataset"/>

I think the last variant of this is what you want though
$input.is_of_type( ext ). You don't need to know the full module path
to the parent type - you are referring to it using the same extension
the rest of the tool uses and it doesn't require the use of $__app__
which... well we shouldn't be exposing to tools - it is not safe and
is a hindrance to ensuring backward compatibility.

Hope this helps.

-John


On Tue, Aug 12, 2014 at 11:53 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> I've just uploaded a simple sequence composition tool to the
> Test Tool Shed:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition
> https://github.com/peterjc/pico_galaxy/commit/45669446f5a14fd90a8a0d9d7430499de2fb3493
>
> This accepts multiple input in FASTA, FASTQ, or SFF format -
> and allows a mixture of these:
>
> <inputs>
>     <param name="input_file" type="data" format="fasta,fastq,sff"
> multiple="true" label="Sequence file" help="FASTA, FASTQ, or SFF
> format." />
> </inputs>
>
> In order to build the command line string, I am currently using this
> for loop:
>
> <command interpreter="python">
> seq_composition.py -o "$output_file"
> ##For loop over inputs
> #for i in $input_file
> --$i.ext "${i}"
> #end for
> </command>
>
> This results in things like this being run:
>
> seq_composition.py -o XXX.dat --fastqsanger XXX.dat --sff XXX.dat
>
> This works, but means my Python script has to know about not just
> the core data types that I specified in my input parameter XML
> (fasta,fastq,sff) but also any subclasses (e.g. fastqsanger).
>
> It seems what I want/need would be something along these lines
> in pseudo-code to map any datatype which is a subclass for fastq
> to use a single command line option:
>
> <command interpreter="python">
> seq_composition.py -o "$output_file"
> ##For loop over inputs
> #for i in $input_file
> #if isinstance($i.datatype, fastq):
> --fastq "${i}"
> #else
> --$i.ext "${i}"
> #end if
> #end for
> </command>
>
> This mock example borrows from the Python isinstance function,
> but of course some Galaxy datatypes are defined as subclasses
> at the XML level rather than literally at the Python class level.
>
> This should result in getting the following regardless of which
> flavour of FASTQ the input dataset had assigned:
>
> seq_composition.py -o XXX.dat --fastq XXX.dat --sff XXX.dat
>
> Does anyone have any Tool XML examples probing an input file's
> datatype in this way?
>
> Peter
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