comparison tarfast5.xml @ 2:e660e8605dd8 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"

1:436f11e1ed6d

<tool id="tarfast5" name="tarfast5" version="0.4">
  <description></description>
  <requirements>
        <requirement type="package" version="2.6">pigz</requirement>
        <requirement type="package" version="1.34">tar</requirement>
  </requirements>

  </stdio>
  <command detect_errors="exit_code"><![CDATA[
        #for $file in $inputs:
            ln -s $file ${file.element_identifier}.h5 &&
        #end for
            export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
            tar -cvh --use-compress-program=pigz -f $compressed_output *.h5
  ]]></command>
 <inputs>
    <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" />
 </inputs>

 <outputs>
    <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" />
</outputs>

    <tests>
        <test> <!-- 0 -->
            <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
            <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" />
        </test>
    </tests>
<help>

**What it does**

2:e660e8605dd8

<tool id="tarfast5" name="tarfast5" version="0.5.2">
  <description></description>
  <requirements>
        <requirement type="package" version="2.6">pigz</requirement>
        <requirement type="package" version="1.34">tar</requirement>
  </requirements>

  </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>

 <outputs>
    <data format="fast5.tar" name="output" label="Archive of fast5" >
        <change_format>
            <when input="output_format" value="gzip" format="fast5.tar.gz"/>
        </change_format>
    </data>


</outputs>

    <tests>
        <test> <!-- tar -->
            <param name="inputs" value="F1.fast5.h5" ftype="h5" />
            <param name="output_format" value="tar" />
            <output file="archive.tar" name="output" compare="sim_size" delta="3000" />
        </test>

        <test> <!-- tar.gz -->
            <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
            <param name="output_format" value="gzip" />
            <output file="archive.tar.gz" name="output" compare="sim_size" delta="3000" />
        </test>
    </tests>
<help>

**What it does**