comparison tarfast5.xml @ 4:56b8caf469f3 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"

3:75ae798e310b

<tool id="tarfast5" name="tarfast5" version="0.5.3">
  <description></description>
  <requirements>
        <requirement type="package" version="2.6">pigz</requirement>
        <requirement type="package" version="1.34">tar</requirement>
  </requirements>
  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[
        #for $file in $inputs:
            ln -s $file ${file.element_identifier}.h5 &&
        #end for
        #if $output_format == "gzip":
            export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
            tar -cvh --use-compress-program=pigz -f $output *.h5
        #else:
            tar -cvh -f $output *.h5
        #end if
  ]]></command>
 <inputs>
    <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" />
    <param name="output_format" type="select" label="compression of the tar archive" display="radio">
        <option value="tar">tar (no compression)</option>
        <option value="gzip" selected="true">tar.gz</option>
    </param>
 </inputs>

4:56b8caf469f3

<tool id="tarfast5" name="tarfast5" version="0.6.0">
  <description></description>
  <requirements>
        <requirement type="package" version="2.6">pigz</requirement>
        <requirement type="package" version="1.34">tar</requirement>
  </requirements>
  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[
        #for $file in $inputs:
            ln -s $file ${file.element_identifier}.fast5 &&
        #end for
        #if $output_format == "gzip":
            export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
            tar -cvh --use-compress-program=pigz -f $output *.fast5
        #else:
            tar -cvh -f $output *.fast5
        #end if
  ]]></command>
 <inputs>
    <param name="inputs" type="data" format="h5,fast5.tar" label="fast5 sequence files" multiple="true" />
    <param name="output_format" type="select" label="compression of the tar archive" display="radio">
        <option value="tar">tar (no compression)</option>
        <option value="gzip" selected="true">tar.gz</option>
    </param>
 </inputs>