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comparison lcb_split.xml @ 1:5d9bc33ec5d3 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:54:34 +0000
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0:21d00cf83137 1:5d9bc33ec5d3
1 <tool id="edu.tamu.cpt.xmfa.split" name="Split LCBs into smaller LCBs" version="@WRAPPER_VERSION@.0">
2 <description/>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 'python $__tool_directory__/lcb_split.py'
10 @XMFA_INPUT@
11 --window_size '$window_size'
12 --threshold '$threshold'
13 > '$output'
14 ]]></command>
15 <inputs>
16 <expand macro="xmfa_input"/>
17 <param type="integer" name="window_size" value="10" label="Default window size generating smaller LCBs"/>
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"/>
19 </inputs>
20 <outputs>
21 <data format="xmfa" name="output"/>
22 </outputs>
23 <help><![CDATA[
24 **What it does**
25
26 Helps reduce large and non-sensical protein LCBs into real protein alignments.
27
28 **WARNING**
29
30 Probably does not work if you have - strand genes. Need to test.
31
32 ]]></help>
33 <!-- TODO -->
34 <expand macro="citations"/>
35 </tool>