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author cpt
date Fri, 05 Jan 2024 05:58:11 +0000
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1 <tool id="edu.tamu.cpt.xmfa.split" name="Split LCBs into smaller LCBs" version="@WRAPPER_VERSION@.0">
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2 <description/>
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3 <macros>
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4 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 'python $__tool_directory__/lcb_split.py'
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10 @XMFA_INPUT@
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11 --window_size '$window_size'
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12 --threshold '$threshold'
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13 > '$output'
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14 ]]></command>
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15 <inputs>
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16 <expand macro="xmfa_input"/>
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17 <param type="integer" name="window_size" value="10" label="Default window size generating smaller LCBs"/>
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18 <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"/>
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19 </inputs>
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20 <outputs>
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21 <data format="xmfa" name="output"/>
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22 </outputs>
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23 <help><![CDATA[
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24 **What it does**
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26 Helps reduce large and non-sensical protein LCBs into real protein alignments.
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28 **WARNING**
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30 Probably does not work if you have - strand genes. Need to test.
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32 ]]></help>
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33 <!-- TODO -->
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34 <expand macro="citations"/>
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35 </tool>