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