view srf2fastq/srf2fastq.xml @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

<tool id="srf2fastq" name="SRF to FASTQ" version="1.0.1">
  <description>conversion</description>
  <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2
  </command>
  <inputs>
    <param name="input1" type="data" format="srf" label="Select SRF Archive"/>
    <param name="filter" label="Filter out bad reads (QC fail)?" type="select">
      <option value="Y" selected="True">Yes</option>
      <option value="N">No</option>
    </param>
    <param name="paired" label="Is this Paired-end run?" type="select">
      <option value="Y">Yes</option>
      <option value="N" selected="True">No</option>
    </param>
  </inputs>
  <outputs>
      <data format="fastqsanger" name="out_file1"/>
      <data format="fastqsanger" name="out_file2">
         <filter>paired == "Y"</filter>
      </data>
  </outputs>
<help>

**What it does**

Converts SRF Archives into fastq files

--------

**Explanation of parameters**

**Filter out bad reads (QC fail)?** - QC failing reads are marked in SRF file and can be excluded in fastq generation.

**Is this Paired-end run?** - Select Yes if the SRF contains paired-end data. This creates two separate fastq files.

</help>
</tool>