comparison fastq_dump_paired.xml @ 4:6c9eb322892d draft

Uploaded

3:b3e5722aa5e7

<tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1">
    <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>
    <inputs>
        <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
    </inputs>
    <outputs>
       <data format="fastqsanger" label="${tool.name} on ${on_string}: ${accession_number} Forward Reads" name="forward_reads" from_work_dir="R1.fastq" >
       </data>
       <data format="fastqsanger" label="${tool.name} on ${on_string}: ${accession_number} Reverse Reads" name="reverse_reads" from_work_dir="R2.fastq" >
       </data>
    </outputs>
    
    <tests>
    <!-- Empty -->

::

  fastq-dump --log-level fatal --split-3 --accession accession_number


Data is stored in fastqsanger format.

------

.. class:: infomark

4:6c9eb322892d

<tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1.1">
    <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>
    <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 -->

::

  fastq-dump --log-level fatal --split-3 --accession accession_number


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