Mercurial > repos > iuc > hyphy_conv

annotate hyphy_conv.xml @ 1:5d89d7b76ca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
author iuc
date Tue, 20 Apr 2021 19:44:05 +0000
parents 6a19eda9b9cb
children 67edc6d534c3
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6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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1 <?xml version="1.0"?>
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5d89d7b76ca7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
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2 <tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy1" profile="19.09">
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6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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3 <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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4 <macros>
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5 <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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6 </macros>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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7 <expand macro="requirements"/>
6a19eda9b9cb "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[
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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9 cp '$input_file' conv_input.fa &&
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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10 hyphy conv
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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11 '$gencodeid'
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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12 '$deletions'
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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13 conv_input.fa
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5d89d7b76ca7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
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14 aa.nex
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15 > ./conv.log
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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16 @ERRORS@
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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17 ]]></command>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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18 <inputs>
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19 <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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20 <param name="save_log" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Save the conversion log to your history" />
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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21 <expand macro="gencode"/>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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22 <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"/>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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23 </inputs>
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24 <outputs>
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25 <data name="conv_log" format="txt" from_work_dir="conv.log">
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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26 <filter>save_log</filter>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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27 </data>
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28 <data name="proteins" format="nex" from_work_dir="aa.nex" />
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29 </outputs>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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30 <tests>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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31 <test>
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32 <param name="input_file" ftype="fasta" value="conv-in1.fa"/>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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33 <param name="deletions" value="Keep Deletions" />
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34 <output name="proteins" file="conv-out1.nex" />
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35 </test>
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36 </tests>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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37 <help><![CDATA[
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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38 HyPhy-CONV: Translate an in-frame codon alignment to proteins
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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39 =============================================================
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40
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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41 This tool takes a codon-aligned fasta file and outputs the amino acid sequence
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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42 it represents, with the option to keep or skip deletions in the input file.
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43 ]]>
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44 </help>
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45 <expand macro="citations" />
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46 </tool>
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47