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1 <tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0">
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2 <description>on a reference tree</description>
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6
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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 <requirements>
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7 <requirement type="package">yapp_env</requirement>
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8 </requirements>
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6
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9 <stdio>
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10 <expand macro="basic_errors"/>
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11 </stdio>
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12 <version_command>echo "pplacer $(pplacer --version)"</version_command>
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13 <command interpreter="bash">
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14 pplacer-wrapper.sh ${config}
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15 </command>
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16 <inputs>
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17 <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
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18 <param name="query_seqs" type="data" format="fasta" label="Query alignment"/>
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19 </inputs>
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20 <outputs>
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21 <data name="placed_seqs" format="jplace" label="Placed sequences"/>
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22 </outputs>
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23 <configfiles>
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24 <configfile name="config">
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25 REFPKG="${refpkg.extra_files_path}"
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26 QUERY_SEQS="${query_seqs}"
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27
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28 PLACED_SEQS="${placed_seqs}"
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29 </configfile>
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30 </configfiles>
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31 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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32 help-template.rst for examples of commonly-used sections in other Galaxy
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33 tools. -->
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34 <help>
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35
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36 .. class:: infomark
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37
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38 **What it does**
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39
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40 This tool places query sequences on a fixed reference phylogenetic tree
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41 according to a reference alignment, producing taxonomic annotations which can
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42 be used for classification and visualization.
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43
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44 </help>
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45 <citations>
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46 <expand macro="cite_pplacer"/>
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47 </citations>
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48 </tool>
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