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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:15:02 +0000
parents dc8875a13914
children
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31e7f5a25db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>in a multiple alignment using HyPhy</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 hyphy '$__tool_directory__/scripts/strike-ambigs.bf'
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9 --alignment '$alignment' --output '$output'
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10 @ERRORS@
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11 ]]></command>
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12 <inputs>
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31e7f5a25db3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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13 <param argument="--alignment" type="data" format="fasta" label="Input alignment" />
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14 </inputs>
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15 <outputs>
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16 <data name="output" format="fasta" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="alignment" ftype="fasta" value="strike-ambigs-in1.fa"/>
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21 <output name="output" file="strike-ambigs-out1.fa" />
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22 </test>
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23 <test>
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24 <param name="alignment" ftype="fasta" value="strike-ambigs-in2.fa"/>
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25 <output name="output" file="strike-ambigs-out2.fa" />
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 HyPhy Strike-Ambigs
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30 ===================
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32 Reads an alignment of coding sequences and replaces any ambiguous codons with ---.
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33
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34 Note: The input fasta must be aligned along codon boundaries.
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35 ]]></help>
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36 <expand macro="citations">
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37 <citation type="doi">10.1093/bioinformatics/bti079</citation>
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38 </expand>
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39 </tool>