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annotate hyphy_conv.xml @ 11:beeeed9665ea draft default tip

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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 15:10:54 +0000
parents 079ea2eb9ae4
children
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11
beeeed9665ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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1 <tool id="hyphy_conv" name="HyPhy-Conv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2 <description>translate an in-frame codon alignment to proteins</description>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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3 <macros>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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4 <import>macros.xml</import>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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5 </macros>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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6 <expand macro="requirements"/>
9ce3d6d4bd0e "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[
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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8 cp '$input_file' conv_input.fa &&
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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9 hyphy conv
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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10 '$gencodeid'
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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11 '$deletions'
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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12 conv_input.fa
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c1d24ff838c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
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13 aa.nex
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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14 @ERRORS@
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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15 ]]></command>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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16 <inputs>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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17 <param name="input_file" type="data" format="fasta" label="Input codon alignment"/>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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18 <expand macro="gencode"/>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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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"/>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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20 </inputs>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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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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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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23 </outputs>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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24 <tests>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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25 <test>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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26 <param name="input_file" ftype="fasta" value="conv-in1.fa"/>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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27 <param name="deletions" value="Keep Deletions" />
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28 <output name="proteins" file="conv-out1.nex" />
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29 </test>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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30 </tests>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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31 <help><![CDATA[
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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32 HyPhy-CONV: Translate an in-frame codon alignment to proteins
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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33 =============================================================
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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35 This tool takes a codon-aligned fasta file and outputs the amino acid sequence
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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36 it represents, with the option to keep or skip deletions in the input file.
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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37 ]]>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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38 </help>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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39 <expand macro="citations" />
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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40 </tool>
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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