annotate bundle_collection.xml @ 2:705ebd286b57 draft default tip

"planemo upload commit 7761f1e59039279728185e751f1a51b56fe14cb0"

<tool id="bundle_collection" name="Bundle Collection" version="1.3.0">
  <description>Package up and download a collection of files as a single archive.</description>
  <requirements>
    <requirement type="package" version="2.50">perl-getopt-long</requirement>
    <requirement type="package" version="1.69">perl-pod-usage</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
    perl '$__tool_directory__/bundle_collection.pl' -h '$html_file' -p '$html_file.files_path'

    #if $singles_or_list.type == "list":

      #if $singles_or_list.input:
        #for $f in $singles_or_list.input.keys
          -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]"
          #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None"
            #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index
            -i "$bamind"
          #end if
        #end for
      #end if
    #elif $singles_or_list.type == "singles":
      #for $dataset in $singles_or_list.single_files
        #if $dataset.single_file:
          -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file"
        #end if

        #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None"
          #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index
          -i "$bamind"
        #end if
      #end for
    #end if
  ]]></command>

  <inputs>
    <conditional name="singles_or_list">
      <param name="type" type="select" label="Bundle type">
        <option value="singles">Individual datasets</option>
        <option value="list">List Collection </option>
      </param>
      <when value="singles">
        <repeat name='single_files' title='Single dataset(s)'>
          <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/>
        </repeat>              
      </when>
      <when value="list">
        <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/>
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data name="html_file" format="html" label="Bundled Collection" />
  </outputs>

  <tests>
    <test>
      <conditional name="singles_or_list">
        <param name="type" value="singles" />
        <repeat name="single_files">
          <param name="single_file" value="first.txt" />
        </repeat>
      </conditional>
      <output name="html_file" file="out-1.html" />
    </test>
    <test>
      <conditional name="singles_or_list">
        <param name="type" value="singles" />
        <repeat name="single_files">
          <param name="single_file" value="first.txt" />
        </repeat>
        <repeat name="single_files">
          <param name="single_file" value="second.txt" />
        </repeat>
      </conditional>
      <output name="html_file" file="out-2.html" />
    </test>
    <test>
      <conditional name="singles_or_list">
        <param name="type" value="list" />
        <param name="input">
          <collection type="list">
            <element name="first.txt" value="first.txt"/>
            <element name="second.txt" value="second.txt"/>
          </collection>
        </param>
      </conditional>
      <output name="html_file" file="out-2.html" />
    </test>
  </tests>

  <help><![CDATA[
    ***What it does**

    This tool will bundle up files in a list collection into a downloadable zip file

    Author: Mariam Iskander, Jen Cabral, and Aaron Petkau (Public Health Agency of Canada).
    ]]>
  </help>

  <citations>
    <citation type="bibtex">
      @UNPUBLISHED{PHAC2020,
        author = "Public Health Agency of Canada",
        title = "Bundle Collections",
        year = "2020",
        url = {https://github.com/phac-nml/galaxy_tools}
      }
    </citation>
  </citations>

</tool>