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1 <tool id="PHYLO_preclassification" name="Generate database" version="1.2.0">
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2 <description>for classification</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
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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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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 preclassification-wrapper.sh ${config}
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15 </command>
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16 <inputs>
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17 <param name="dedup_info" type="data" format="csv" label="Deduplication info"/>
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18 <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
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19 <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/>
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20 <param name="placed_seqs" type="data" format="jplace" label="Placements"/>
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21 </inputs>
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22 <outputs>
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23 <data name="reduped_seqs" format="jplace" label="Reduped placements"/>
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24 <data name="class_db" format="sqlite3" label="Placement database"/>
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25 </outputs>
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26 <configfiles>
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27 <configfile name="config">
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28 DEDUP_INFO="${dedup_info}"
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29 REFPKG="${refpkg.extra_files_path}"
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30 NBC_SEQS="${nbc_seqs}"
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31 PLACED_SEQS="${placed_seqs}"
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32
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33 REDUPED_SEQS="${reduped_seqs}"
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34 CLASS_DB="${class_db}"
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35 </configfile>
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36 </configfiles>
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37 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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38 help-template.rst for examples of commonly-used sections in other Galaxy
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39 tools. -->
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **What it does**
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45
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46 This tool outputs the classifications made by ``pplacer`` to a database for use
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47 in taxonomic classification.
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48
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49 </help>
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6
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50 <citations>
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51 <expand macro="cite_pplacer"/>
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52 </citations>
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53 </tool>
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