[galaxy-dev] Adding a5_pipeline.pl to galaxy

[Raphenya, Amogelang]

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 e:  raphe...@mcmaster.ca  skype: amos_raphenya

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