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1 <tool id="PHYLO_usearch" name="Analyze sequences" version="1.1.0">
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2 <description>with USEARCH</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 <stdio>
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7 <expand macro="basic_errors"/>
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8 </stdio>
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9 <version_command>/home/matsengrp/local/bin/usearch6_64 --version</version_command>
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10 <command interpreter="bash">
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11 usearch-wrapper.sh $config
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12 </command>
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13 <inputs>
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14 <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
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15 <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
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16 </inputs>
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17 <outputs>
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18 <data format="csv" name="usearch_hits" label="USEARCH hits"/>
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19 <data format="csv" name="usearch_groups" label="USEARCH groups"/>
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20 </outputs>
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21 <configfiles>
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22 <configfile name="config">
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23 INPUT_SEQS="${input_seqs}"
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24 CLASS_DB="${class_db}"
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25
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26 USEARCH_HITS="${usearch_hits}"
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27 USEARCH_GROUPS="${usearch_groups}"
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28 </configfile>
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29 </configfiles>
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30 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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31 help-template.rst for examples of commonly-used sections in other Galaxy
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32 tools. -->
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33 <help>
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34
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35 .. class:: infomark
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36
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37 **What it does**
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38
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39 This tool queries large sequence databases for target sequences and assigns
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40 those sequences to clusters.
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41
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42 </help>
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6
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43 <citations>
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44 <expand macro="cite_usearch"/>
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45 </citations>
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46 </tool>
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