<tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1.4">
    <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description>
    <requirements>
       <!-- Should just use the samtools that's installed in the path -->
       <requirement type="binary">fastq-dump</requirement>
    </requirements>
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
## ! We only have a simple single command here.
fastq-dump --log-level fatal --split-3 --accession ${accession_number} --ncbi_error_report never;
ls -lh | grep ${accession_number};
mv -v ${accession_number}_1.fastq R1.fastq;
mv -v ${accession_number}_2.fastq R2.fastq;
    </command>
    <inputs>
        <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
    </inputs>
    <outputs>
       <data format="fastqsanger" label="${accession_number}_1" name="forward_reads" from_work_dir="R1.fastq" >
       </data>
       <data format="fastqsanger" label="${accession_number}_2" name="reverse_reads" from_work_dir="R2.fastq" >
       </data>
    </outputs>
    
    <tests>
    <!-- Empty -->
    </tests>

    <help>

.. class:: infomark

**What it does**

Performs a fastq-dump with the split-3 option.

::

  fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never


Data is stored in fastqsanger format. 

The metadata is now named to make it easier for collection lists to
fetch when you search for reads in your history. 

------

.. class:: infomark

**Tool Author**

Mando Rodriguez

    </help>
</tool>