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comparison cpt_convert_xmfa/xmfa2tbl.xml @ 0:06d8e28d0bd7 draft default tip

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author cpt
date Fri, 10 Jun 2022 08:49:43 +0000
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1 <?xml version="1.0"?>
2 <tool id="xmfa2tbl" name="Convert XMFA to percent identity table" version="19.1.0.0">
3 <description></description>
4 <macros>
5 <import>macros.xml</import>
6 <import>cpt-macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[
10 python $__tool_directory__/xmfa2tbl.py
11 $dice
12 @XMFA_INPUT@
13 @XMFA_FA_INPUT@
14
15 > $output
16 ]]></command>
17 <inputs>
18 <expand macro="xmfa_input" />
19 <expand macro="xmfa_fa_input" />
20 <param type="boolean" label="use dice method in percent similarity calculation"
21 truevalue="--dice" falsevalue="" name="dice" help="The dice method alters the total similarity calculation to reflect the length of both sequences. The default for this option is true."/>
22 </inputs>
23 <outputs>
24 <data format="tabular" name="output" />
25 </outputs>
26 <tests>
27 <test>
28 <param name="xmfa" value="test.xmfa"/>
29 <param name="sequences" value="test.fa" />
30 <output name="output" file="xmfa2tbl_out.tsv"/>
31 </test>
32 <test>
33 <param name="dice" value="true"/>
34 <param name="xmfa" value="test.xmfa"/>
35 <param name="sequences" value="test.fa" />
36 <output name="output" file="xmfa2tbl_out_dice.tsv"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40 **What it does**
41
42 This tool compares nucleotide sequences within an input XMFA file and outputs a table reflecting
43 the percent nucleotide identity between every sequence pair. Total similarity is based on
44 regions of similarity called locally collinear blocks, or LCBs. There is no penalty for gaps.
45
46 **Options**
47 The dice method uses the following formula to normalize considering both sequences in the pairwise comparison::
48
49 2 * number of identical matches / (query sequence length + subject sequence length)
50
51 ]]></help>
52 <expand macro="citations-2020" />
53 </tool>