<tool id="compalignp" name="Compalignp" version="1.0">
    <description>Fractional identities between alignments</description>
    <requirements>
        <requirement type="package" version="1.0">compalignp</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>
    <command>
<![CDATA[
    compalignp
        -t $rna_alignment_target
        -r $rna_alignment_reference
    > $output
]]>
    </command>
    <inputs>
        <param format="clustalw,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
        <param format="clustalw,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="rna_alignment_target" value="eukaryotic-trnas_2.1.clustal"/>
            <param name="rna_alignment_reference" value="eukaryotic-trnas_2.1.clustal"/>
            <output name="output" file="eukaryotic-trnas_2.1.out"/>
        </test>
    </tests>
    <help>
<![CDATA[
**compalignp**

> Paranoia version of squids compalign. 

Compute fractional "identity" between trusted alignment and test alignment
Identity of the multiple sequence alignments is defined as
the averaged identity over all N(N-1)/2 pairwise alignments.


]]>
    </help>
<citations>
  <citation type="doi">10.1186/1748-7188-1-19</citation>
</citations>
</tool>