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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 15:12:39 +0000
parents fa913c2975da
children
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91cf1290ba6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_annotate" name="Annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>a newick tree with 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 cp '$input_tree' input.nhx &&
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9 cp '$compressed_msa' input.$compressed_msa.extension &&
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10 cp '$__tool_directory__/scripts/annotator.bf' annotator.bf &&
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11 hyphy annotator.bf
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12 input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree_
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13 @ERRORS@
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14 ]]></command>
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15 <inputs>
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16 <param name="input_tree" type="data" format="nhx" label="Input tree" />
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17 <param name="compressed_msa" type="data" format="fasta,fasta.gz" label="Multiple alignments" />
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18 <param name="root" type="text" optional="false" value="REFERENCE" label="Root node" />
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19 <param name="label" type="text" optional="false" value="Tree" label="Label for tree" />
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20 </inputs>
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21 <outputs>
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22 <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree_int.nwk" label="${tool.name} on ${on_string} Labeled tree (int)" />
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23 <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree_clade.nwk" label="${tool.name} on ${on_string} Labeled tree (clade)" />
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24 <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree_full.nwk" label="${tool.name} on ${on_string} Labeled tree (full)" />
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25 <data name="labeled_tree_json" format="hyphy_results.json" from_work_dir="labeled_tree_labels.json" label="${tool.name} on ${on_string} Labels" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="compressed_msa" ftype="fasta.gz" value="annotate-in1.fa.gz"/>
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30 <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
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31 <param name="root" value="REFERENCE" />
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32 <param name="label" value="Annotated" />
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33 <output name="labeled_tree_int" file="annotate-out1-int.nhx" />
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34 <output name="labeled_tree_full" file="annotate-out1-full.nhx" />
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35 <output name="labeled_tree_clade" file="annotate-out1-clade.nhx" />
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36 <output name="labeled_tree_json" file="annotate-out1.json" />
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 HyPhy Annotate
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41 ==============
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42
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43 Given a set of alignments and a newick tree, this tool produces an annotated tree with
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44 the specified root node and label.
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45 ]]></help>
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46 <expand macro="citations">
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47 <citation type="doi">10.1093/molbev/msv022</citation>
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48 </expand>
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49 </tool>