Mercurial > repos > iuc > hyphy_strike_ambigs

annotate hyphy_strike_ambigs.xml @ 0:7c86ceaf523c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:27:46 +0000
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children dc8875a13914
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7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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1 <?xml version="1.0"?>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2 <tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@VERSION@">
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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3 <description>in a multiple alignment using HyPhy</description>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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4 <macros>
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5 <import>macros.xml</import>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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6 </macros>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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7 <expand macro="requirements"/>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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8 <command detect_errors="exit_code"><![CDATA[
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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9 hyphy '$__tool_directory__/scripts/strike-ambigs.bf'
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10 --alignment '$alignment' --output '$output'
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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11 @ERRORS@
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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12 ]]></command>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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13 <inputs>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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14 <param name="alignment" type="data" format="fasta" label="Input alignment" />
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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15 </inputs>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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16 <outputs>
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17 <data name="output" format="fasta" />
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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18 </outputs>
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19 <tests>
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20 <test>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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21 <param name="alignment" ftype="fasta" value="strike-ambigs-in1.fa"/>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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22 <output name="output" file="strike-ambigs-out1.fa" />
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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23 </test>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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24 <test>
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25 <param name="alignment" ftype="fasta" value="strike-ambigs-in2.fa"/>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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26 <output name="output" file="strike-ambigs-out2.fa" />
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27 </test>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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28 </tests>
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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29 <help><![CDATA[
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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30 HyPhy Strike-Ambigs
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31 ===================
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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32
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33 Reads an alignment of coding sequences and replaces any ambiguous codons with ---.
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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34
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35 Note: The input fasta must be aligned along codon boundaries.
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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36 ]]></help>
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37 <expand macro="citations">
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38 <citation type="doi">10.1093/bioinformatics/bti079</citation>
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39 </expand>
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40 </tool>