view gzip.xml @ 0:401afd3c5220 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7

<tool id="justgzip" name="Gzip sequence datasets" version="0.1.0">
  <description></description>
  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[  
gzip -ck '${input1}' >  $output
  ]]></command>
  <inputs>
      <param format="fastq" name="input1" type="data" label="Input file" help="file to compress" />
      <param name="datatype" type="select" label="Input file datatype" help="Input file datatype" >
          <option value="sanger" >fastqsanger </option>
          <option value="illumina" >fastqillumina </option>
          <option value="fastq" selected="true" >fastq </option>
      </param>
  </inputs>
  <outputs>

   <data name="output" format="fastq.gz" label="$input1.name " >
   <change_format>
       <when input="datatype" value="sanger" format="fastqsanger.gz" />
       <when input="datatype" value="illumina" format="fastqillumina.gz" />
   </change_format>
   </data>
  </outputs>
  <tests>
      <test>
          <param name="input1" value="file1" ftype="fastq" />
          <param name="datatype" value="fastq" />
          <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/>
      </test>
      <test>
          <param name="input1" value="file1" ftype="fastqsanger" />
          <param name="datatype" value="sanger" />
          <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" />
      </test>   

  </tests>
  <help>

.. class:: infomark

**What it does**

Just **gzip** fastq, fastqillumina and fastqsanger datasets.
    
  </help>
</tool>