view cpt_xmfa_split/lcb_split.xml @ 0:21d00cf83137 draft

Uploaded

<?xml version="1.0"?>
<tool id="edu.tamu.cpt.xmfa.split" name="Split LCBs into smaller LCBs" version="@WRAPPER_VERSION@.0">
	<description></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>