If you have a wrapper script, then you can do it there.

It is also possible in the XML directly by building a composite
command with && separators (which must be escaped as
&& or using CDATA), e.g.

https://github.com/galaxyproject/tools-devteam/blob/master/tools/samtool_filter2/samtool_filter2.xml
(nice BAM and BAI example)

https://github.com/galaxyproject/tools-devteam/blob/master/tools/freebayes/freebayes.xml
(does a lot of symlinks)

https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/multiCov.xml
(part of a for loop for multiple BAM and BAI files)

Note you can't use <command interpreter="..."> in this
style as the first command is the shell command ln.

Peter


On Fri, Oct 2, 2015 at 11:17 AM, Martin Vickers <mj...@aber.ac.uk> wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Peter,
>
> Thanks for the reply. Are there any examples of this in action? Is it done
> in the xml wrapper somewhere or do I need to write a script that does this
> and then call the Rscript?
>
> Cheers,
>
> Martin
>
> On 10/02/2015 11:13 AM, Peter Cock wrote:
>> Creating symlinks with normal extensions is a common
>> approach here where the Galaxy filenames won't work.
>>
>> Peter
>>
>> On Fri, Oct 2, 2015 at 10:57 AM, Martin Vickers <mj...@aber.ac.uk> wrote:
>>>
>> Hi all,
>>
>> I've been tasked with getting someone's R script working in our galaxy
>> installation and I'm struggling to resolve an issue with an bioconductor
>> function that appears to not like the galaxy naming convention (e.g.
>> dataset_2.dat) for the bam index file.
>>
>> The R script can run from the command line like this;
>>
>>     Rscript script.R input1.xls alignment.bam alignment.bai p
>>
>> so I have created a wrapper using planemo that does this, and that's fine.
>>
>> The problem is, when I run the script in galaxy, I get the following error
>> from R;
>>
>> Error in value[[3L]](cond) :
>>     failed to open BamFile: failed to load BAM index
>>     file: /tmp/tmpdP2eBC/files/000/dataset_3.dat
>> Calls: f_oGRSeparateStrands ... tryCatch -> tryCatchList -> tryCatchOne ->
>> <Anonymous>
>> In addition: Warning messages:
>> In doTryCatch(return(expr), name, parentenv, handler) :
>>     [bam_index_load] fail to load BAM index.
>> Execution halted
>>
>> The function that reads the bam + bai file in the script is;
>>
>> bam = readGAlignments(file=bam.file, index=bai.file,
>> param=ScanBamParam(which=gr.signal))
>>
>> http://www.rdocumentation.org/packages/GenomicRanges/html/GAlignments.html
>>
>> In the documentation for this function it states the following;
>>
>> "file, index, The path to the BAM file to read, and to the index file of
>> the
>> BAM file to read, respectively. The latter is given /without/ the '.bai'
>> extension. See |scanBam
>> <http://www.rdocumentation.org/packages/Rsamtools/functions/scanBam.html>|
>> for more information."
>>
>> I've played around with this a little and from the command line I've been
>> successfully able to run the script to completion when the input bam file
>> and bai are completely different names;
>>
>> e.g.
>>
>> Rscript script.R input1.xls something.bam meh.bai p
>>
>> but I can't run it if I change the extension, e.g.
>>
>> Rscript script.R input1.xls something.dat meh.dat p
>> Error in value[[3L]](cond) :
>>
>>     failed to open BamFile: failed to load BAM index
>>     file: /tmp/tmpdP2eBC/files/000/dataset_3.dat
>> Calls: f_oGRSeparateStrands ... tryCatch -> tryCatchList -> tryCatchOne ->
>> <Anonymous>
>> In addition: Warning messages:
>> In doTryCatch(return(expr), name, parentenv, handler) :
>>     [bam_index_load] fail to load BAM index.
>> Execution halted
>>
>>
>> Does anyone have any experience of resolving this kind of issue?
>>
>>
>>>
>>>
>>> ___________________________________________________________
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>
> - --
>
> - --
> Dr. Martin Vickers
>
> Data Manager/HPC Systems Administrator
> Institute of Biological, Environmental and Rural Sciences
> IBERS New Building
> Aberystwyth University
> SY23 3FG
>
> w: http://www.martin-vickers.co.uk/
> e: mj...@aber.ac.uk
> t: 01970 62 2807
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