Hi,

When you use ${output}, Galaxy creates a file in database/file/XXXX/dataset_YYY.dat.
Your script seem to need a directory or maybe a prefix like "output".

So when the script generate its output filename. You can use the from_work_dir attribute of <data>

 
So, I guess something like that:


<tool id="a5_miseq" name="A5 MiSeq" version="0.1.0">

  <description>assemble microbial fastQ to fatsA</description>

  <command interpreter="perl">a5_pipeline.pl ${file1} ${file2} output </command>

  <inputs>
    <param format="fastq" name="file1" type="data" label="Fastq Sequence files"/>
    <param format="fastq" name="file2" type="data" label="Fastq Sequence files"/>
  </inputs>

<!—- Expected Results 
output.contigs.fasta  <!— This is a text file —>
output.contigs.qvl  <!— This is a text file —>
output.raw1.pe.sort.bam  <!— This is a text file —>
output.tmplibs <!— This is a text file —>
output.assembly_stats.csv  <!— This is a text file —>
output.contigs.fastq  <!— This is a text file —>
output.ec.fastq.gz   <!— This is a compressed file —>
output.raw1.pe.sort.bam.bai  <!— This is a text file —>
output.s1  <!— This is a directory —>
output.s2   <!— This is a directory —>
-->
 <outputs>
    <data format="fasta" name="output_fasta" from_work_dir="output.contigs.fasta" label=“A5 output fastA"/>
    <data format="fastq" name="output_fastq" from_work_dir="output.contigs.fastq" label=“A5 output fastQ”/>
</outputs>

</tool>

Good luck

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
------------------------------------------------------------------



Le 22 janv. 2016 à 15:13, Raphenya, Amogelang <raphenar@mcmaster.ca> a écrit :

Hi All,

I have a problem getting all the outputs in galaxy.

My xml config file looks like this:

<tool id="a5_miseq" name="A5 MiSeq" version="0.1.0">

  <description>assemble microbial fastQ to fatsA</description>

  <command interpreter="perl">a5_pipeline.pl ${file1} ${file2} ${output} </command>

  <inputs>
    <param format="fastq" name="file1" type="data" label="Fastq Sequence files"/>
    <param format="fastq" name="file2" type="data" label="Fastq Sequence files"/>
  </inputs>

<!—- Expected Results 
output.contigs.fasta  <!— This is a text file —>
output.contigs.qvl  <!— This is a text file —>
output.raw1.pe.sort.bam  <!— This is a text file —>
output.tmplibs <!— This is a text file —>
output.assembly_stats.csv  <!— This is a text file —>
output.contigs.fastq  <!— This is a text file —>
output.ec.fastq.gz   <!— This is a compressed file —>
output.raw1.pe.sort.bam.bai  <!— This is a text file —>
output.s1  <!— This is a directory —>
output.s2   <!— This is a directory —>
-->
 <outputs>
    <data format="fasta" name="output" label=“A5 output fastA"/>
    <data format="fastq" name="output" label=“A5 output fastQ”/>
</outputs>

</tool>

I get the following error when running the tool:

../database/files/000/dataset_733.dat already exists and is not a directory.
Please specify a new file path for a base name after the library file or FastQ files.

Any ideas on how to get all the output or some output?

Cheers.
Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1
skype: amos_raphenya

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