view gzip.xml @ 2:285d48249ba2 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d

<tool id="justgzip" name="Gzip datasets" version="2.8+galaxy0" profile="21.01">
  <description></description>

  <requirements>
    <requirement type="package" version="2.8">pigz</requirement>
  </requirements>

  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>

  <command detect_errors="exit_code"><![CDATA[
      pigz --processes \${GALAXY_SLOTS:-4} -c '${input1}' > '$output'
      #if ($input1.ext.startswith("fastq")  and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]:
          #set ext = $input1.ext + ".gz"
      #else
          #set ext = "gz"
      #end if
      && echo '{"output": {"ext": "$ext"}}' >> galaxy.json
  ]]></command>
  <inputs>
      <param format="data" name="input1" type="data" label="Input file" help="file to compress" />
  </inputs>
  <outputs>
      <data name="output" format="auto" label="${input1.name}.gz" />
  </outputs>
  <tests>
      <test>
          <param name="input1" value="file1" ftype="fastq" />
          <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/>
      </test>
      <test>
          <param name="input1" value="file1" ftype="fastqsanger" />
          <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" />
      </test>   
  </tests>

  <help>

.. class:: infomark

**What it does**

Just **gzip** datasets, but does it faster with the multithreaded pigz program !

  Accepted input formats include:
  - fastq
  - fastqsanger
  - fasta
  - paf
  - gff3
  - nii1
  - nii2
  - gii
  - tabular
  - txt
  - ...

  </help>
</tool>