Mercurial > repos > iuc > hyphy_conv

annotate hyphy_conv.xml @ 12:71ef72fc6dc4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:43:38 +0000
parents 1fc726fccf7c
children
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1fc726fccf7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_conv" name="HyPhy-Conv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>translate an in-frame codon alignment to proteins</description>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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3 <macros>
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4 <import>macros.xml</import>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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5 </macros>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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6 <expand macro="requirements"/>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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7 <command detect_errors="exit_code"><![CDATA[
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8 cp '$input_file' conv_input.fa &&
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71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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9 ENV="TOLERATE_NUMERICAL_ERRORS=1;" hyphy conv
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10 '$gencodeid'
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11 '$deletions'
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12 conv_input.fa
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13 aa.nex
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14 @ERRORS@
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15 ]]></command>
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16 <inputs>
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17 <param name="input_file" type="data" format="fasta" label="Input codon alignment"/>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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18 <expand macro="gencode"/>
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19 <param name="deletions" type="boolean" truevalue="Keep Deletions" falsevalue="Skip Deletions" label="Keep deletions" help="If this is checked, deletions will be left in the output file"/>
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20 </inputs>
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21 <outputs>
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22 <data name="proteins" format="nex" from_work_dir="aa.nex" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input_file" ftype="fasta" value="conv-in1.fa"/>
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71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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27 <param name="deletions" value="true" />
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28 <output name="proteins" file="conv-out1.nex" />
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 HyPhy-CONV: Translate an in-frame codon alignment to proteins
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33 =============================================================
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35 This tool takes a codon-aligned fasta file and outputs the amino acid sequence
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36 it represents, with the option to keep or skip deletions in the input file.
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37 ]]>
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38 </help>
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39 <expand macro="citations" />
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40 </tool>
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