view removeRNA.xml @ 0:0475e4175855 draft default tip

planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty

<tool id="removeRNA" name="Remove tags from rRNA">
  <description>and other repetitive RNA</description>
  <command interpreter="perl">
	/home/galaxy/tools/CTK/tagoverlap.pl -v  $big -region /home/galaxy/tools/CTK/annotation/genomes/${genome}/annotation/rmsk.RNA.bed  $completeOverlap $reverse $keepTagName $keepScore $sepStr $nonRedundant $input $output
  </command>
  <inputs>
        <param name="input" format="bed" type="data" label="Input BED file (.gz files accepted)" />
	<param name="genome" type="select" label="Genome build name" >
                <option value="hg19">hg19</option>
                <option value="mm10">mm10</option>
        </param>
	<param name="big" type="boolean" truevalue="-big" falsevalue="" checked="yes" label="Either region or tag file is big" />
	<param name="completeOverlap" type="boolean" truevalue="--complete-overlap" falsevalue="" checked="yes" label="Requires complete overlap of the tag with the region" />
	<param name="reverse" type="boolean" truevalue="-r" falsevalue="" checked="yes" label="Reverse mode to print tags without ovrlap with the region" /> 
	<param name="keepTagName" type="boolean" truevalue="--keep-tag-name" falsevalue="" checked="yes" label="Keep tag name" />
	<param name="keepScore" type="boolean" truevalue="--keep-score" falsevalue="" checked="yes" label="Keep tag score" />
	<param name="sepStr"  type="boolean" truevalue="-ss" falsevalue="" checked="no" label="Separate strand" />
	<param name="nonRedundant" type="boolean" truevalue="--non-redundant" falsevalue="" checked="no" label="Remove duplicate tags in output" />
  </inputs>
  <outputs>
        <data name="output" format="bed" label="Remove tags from rRNA on ${on_string}">
        </data> 
  </outputs>

  <help>

.. class:: infomark

**What this tool does**

Remove tags from rRNA and other repetitive RNA. The reason we do this is because ribosomal RNA is a contaminant. 

  </help>
</tool>