view spades_header_fixer.xml @ 2:2cc9e69419d2 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333

<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy1">
	<description>Fixes Spades Fasta ids</description>
  <requirements>
      <requirement type="package" version="4.7.0">sed</requirement>
  </requirements>
  <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1_\2/g" $input >$output</command>
	<inputs>
		<param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
		</inputs>
	<outputs>
		<data name="output" format="fasta"/>
	</outputs>
  <tests>
    <test>
         <param name="input" value="spades_before_1.fasta" />
         <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/>
    </test>
    <test>
         <param name="input" value="spades_before_2.fasta" />
         <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/>
    </test>
  </tests>

	<help><![CDATA[
    SPAdes fasta header fixer
    =======

    The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier.
	]]></help>

  <citations>
        <citation type="bibtex">@ARTICLE{a1,
            title = {SPAdes fasta header fixer},
            author = {Philip Mabon},
            url = {https://github.com/phac-nml/galaxy_tools}
            }
        }</citation>
    </citations>
</tool>