comparison fastq_dump_paired.xml @ 8:daebdda744fc draft

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7:dbee556cf940

<tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1.3">
    <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>

## ! 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>

8:daebdda744fc

<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>

## ! 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;
echo "Deleting any stored files in ~/ncbi";
rm -rf ~/ncbi/*
    </command>
    <inputs>
        <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
    </inputs>
    <outputs>