annotate unzip.xml @ 0:ec30427e0d42 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254

<tool id="unzip" name="Unzip" version="0.1"> 
  <description>Unzip file</description>
  <requirements>
        <requirement type="package">unzip</requirement>
        <requirement type="package">tar</requirement>
  </requirements>
  <command> 
        <![CDATA[  
        mkdir ./out &&
        #if $input_file.is_of_type("zip"):
        unzip "$input_file"
        #if $extract_options['extract_all'] == 'False'
        "$extract_options['pathtofile']"
        #end if
        -d out/
        #end if
        #if $input_file.is_of_type("tar"):
        tar -xf "$input_file"
        #if $extract_options['extract_all'] == 'False'
        "$extract_options['pathtofile']"
        #end if
        -C ./out/
        #end if
        ]]>
  </command>
  <inputs>
    <param label="input_file" name="input_file" type="data" format="zip,tar"/>

    <conditional name="extract_options">
      <param label="Extract single file" name="extract_all" type="select">
          <option selected="True" value="True">All files</option>
          <option value="False">Single file</option>
      </param>
      <when value="True"></when>
      <when value="False">
        <param name="pathtofile" type="text" value="" label="Filepath">
        <sanitizer invalid_char="">
          <valid initial="string.ascii_letters,string.digits">
              <add value="_" />
              <add value="/" />
              <add value="." />
              <add value="/../" />
          </valid>
        </sanitizer>
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>
        <data name="unzipped_single">
          <discover_datasets pattern="__name__" directory="out" visible="true" ext="data" assign_primary_output="true" />
          <filter>extract_options['extract_all'] == 'False'</filter>
        </data>
        <collection name="unzipped" type="list" label="${tool.name} on ${on_string}">
          <discover_datasets pattern="__name__" ext="data" directory="out" visible="false"/>
          <filter>extract_options['extract_all'] == 'True'</filter>
        </collection>
  </outputs>
  <tests>
        <test>
            <param name="input_file" value="input.zip" ftype="zip"/>
            <param name="extract_all" value="False"/>
            <param name="pathtofile" value="input.png"/>
            <output name="unzipped_single" file="input.png" ftype="data" compare="sim_size" />
        </test>
        <test>
            <param name="input_file" value="input.zip" ftype="zip"/>
            <param name="extract_all" value="True"/>
            <output_collection name="unzipped" type="list">
                <element name="input.png" file="input.png" ftype="data" compare="sim_size"/>
                <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/>
            </output_collection>
        </test>
        <test>
            <param name="input_file" value="input.tar" ftype="tar"/>
            <param name="extract_all" value="True"/>
            <output_collection name="unzipped" type="list">
                <element name="input.png" file="input.png" ftype="data" compare="sim_size"/>
                <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/>
            </output_collection>
        </test>
  </tests>   
  <help>
    **What it does**

  Unzip folder to collection.
  </help>
  <citations>
    <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
  </citations>
</tool>