Hello,

I just changed for the CDATA format, but the problem still remains. When I
split by 2, there is no problem, but when I go for 3, it happens the
problem commented before. Here it is the link to the sam/bam file:
 https://dl.dropboxusercontent.com/u/1669701/ejemplo_split.bam

Best regards

On 24 February 2015 at 17:49, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF <ralo...@cipf.es>
> wrote:
> > Hello again,
> >
> > first of all thanks for your help, it is being very useful.
> >
> > What I have done up to now is to copy this method to the class Sequence
> >
> > def get_split_commands_sequential(is_compressed, input_name, output_name,
> > start_sequence, sequence_count):
> >         ...
> >         return [cmd]
> >     get_split_commands_sequential =
> > staticmethod(get_split_commands_sequential)
> >
> > This is something that you suggested.
>
> Good.
>
> > When I run the tool with this configuration:
> >
> > <tool id="bwa_mio" name="map with bwa">
> >   <description>map with bwa</description>
> >   <parallelism method="basic" split_size="3"
> > split_mode="number_of_parts"></parallelism>
> >
> >   <command>
> >       bwa mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
> > $input > $output 2>/dev/null</command>
> >   <inputs>
> >     <param format="fastqsanger" name="input" type="data" label="fastq"/>
> >   </inputs>
> >   <outputs>
> >       <data format="sam" name="output" />
> >   </outputs>
> >
> >   <help>
> >   bwa
> >   </help>
> >
> > </tool>
>
> One minor improvement would be to escape the ">" as "&gt;" in
> your XML, or use the CDATA approach documented here:
>
> https://wiki.galaxyproject.org/Tools/BestPractices
>
> > Everything ends ok, but when I go to check how is the sam, I see that in
> the
> > alingments it is the path of the file, i.e
> > example_split.sam:
> >
> /home/ralonso/galaxy-dist/database/job_working_directory/000/90/task_2/dataset_91.dat:SRR098409.1113446
> > 4 * 0 0 * * 0 0
> >
> TCTGGGTGAGGGAGTGGGGAGTGGGTTTTTGAGGGTGTGTGAGGATGTGTAAGTGGATGGAAGTAGATTGAATGTT
> >
> ############################################################################
> > AS:i:0 XS:i:0
> >
> > you know what  may be going on?
> > If i don't split the file, everything goes correctly.
>
> This sounds to me like there may be a problem with SAM merging?
> Could you share the entire example_split.sam file (e.g. as a gist
> on GitHub, or via dropbox)?
>
> Peter
>



-- 
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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