view usearch.xml @ 6:3c50a937d7c1 draft

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<tool id="PHYLO_usearch" name="Analyze sequences" version="1.1.0">
  <description>with USEARCH</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <version_command>/home/matsengrp/local/bin/usearch6_64 --version</version_command>
  <command interpreter="bash">
    usearch-wrapper.sh $config
  </command>
  <inputs>
    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
    <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
  </inputs>
  <outputs>
    <data format="csv" name="usearch_hits" label="USEARCH hits"/>
    <data format="csv" name="usearch_groups" label="USEARCH groups"/>
  </outputs>
  <configfiles>
    <configfile name="config">
INPUT_SEQS="${input_seqs}"
CLASS_DB="${class_db}"

USEARCH_HITS="${usearch_hits}"
USEARCH_GROUPS="${usearch_groups}"
    </configfile>
  </configfiles>
  <!-- The contents of the help tag is parsed as reStructuredText. Please see
       help-template.rst for examples of commonly-used sections in other Galaxy
       tools. -->
  <help>

.. class:: infomark

**What it does**

This tool queries large sequence databases for target sequences and assigns
those sequences to clusters.

  </help>
  <citations>
    <expand macro="cite_usearch"/>
  </citations>
</tool>