annotate lcb_split.xml @ 1:5d9bc33ec5d3 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

<tool id="edu.tamu.cpt.xmfa.split" name="Split LCBs into smaller LCBs" version="@WRAPPER_VERSION@.0">
    <description/>
    <macros>
        <import>macros.xml</import>
        <import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
'python $__tool_directory__/lcb_split.py'
@XMFA_INPUT@
--window_size '$window_size'
--threshold '$threshold'
> '$output'
]]></command>
    <inputs>
        <expand macro="xmfa_input"/>
        <param type="integer" name="window_size" value="10" label="Default window size generating smaller LCBs"/>
        <param type="float" name="threshold" value="0.7" min="0" max="1" label="Threshold at which a given genome is part of the new small LCBs"/>
    </inputs>
    <outputs>
        <data format="xmfa" name="output"/>
    </outputs>
    <help><![CDATA[
**What it does**

Helps reduce large and non-sensical protein LCBs into real protein alignments.

**WARNING**

Probably does not work if you have - strand genes. Need to test.

]]></help>
    <!-- TODO -->
    <expand macro="citations"/>
</tool>