<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
        </requirements>
    </xml>

    <token name="@TOOL_VERSION@">1.2.11</token>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error in Obitools execution" />
        </stdio>
    </xml>

    <token name="@OBITOOLS_LINK@">
<![CDATA[
--------

**Project links:**

`OBITools`_

.. _OBITools: http://metabarcoding.org/obitools/
]]>
    </token>

    <xml name="attributes">
        <option value="ali_dir" selected="true">ali_dir</option>
        <option value="ali_length">ali_length</option>
        <option value="avg_quality">avg_quality</option>
        <option value="best_match">best_match</option>
        <option value="best_identity">best_identity</option>
        <option value="class">class</option>
        <option value="cluster">cluster</option>
        <option value="complemented">complemented</option>
        <option value="count">count</option>
        <option value="cut">cut</option>
        <option value="direction">direction</option>
        <option value="distance">distance</option>
        <option value="error">error</option>
        <option value="experiment">experiment</option>
        <option value="family">family</option>
        <option value="family_name">family_name</option>
        <option value="forward_error">forward_error</option>
        <option value="forward_match">forward_match</option>
        <option value="forward_primer">forward_primer</option>
        <option value="forward_score">forward_score</option>
        <option value="forward_tag">forward_tag</option>
        <option value="forward_tm">forward_tm</option>
        <option value="genus">genus</option>
        <option value="genus_name">genus_name</option>
        <option value="head_quality">head_quality</option>
        <option value="id_status">id_status</option>
        <option value="merged_star">merged_star</option>
        <option value="merged">merged</option>
        <option value="mid_quality">mid_quality</option>
        <option value="mode">mode</option>
        <option value="obiclean_cluster">obiclean_cluster</option>
        <option value="obiclean_count">obiclean_count</option>
        <option value="obiclean_head">obiclean_head</option>
        <option value="obiclean_headcount">obiclean_headcount</option>
        <option value="obiclean_internalcount">obiclean_internalcount</option>
        <option value="obiclean_samplecount">obiclean_samplecount</option>
        <option value="obiclean_singletoncount">obiclean_singletoncount</option>
        <option value="obiclean_status">obiclean_status</option>
        <option value="occurrence">occurrence</option>
        <option value="order">order</option>
        <option value="order_name">order_name</option>
        <option value="pairend_limit ">pairend_limit </option>
        <option value="partial ">partial </option>
        <option value="rank">rank</option>
        <option value="reverse_error">reverse_error</option>
        <option value="reverse_match">reverse_match</option>
        <option value="reverse_primer">reverse_primer</option>
        <option value="reverse_score">reverse_score</option>
        <option value="reverse_tag">reverse_tag</option>
        <option value="reverse_tm">reverse_tm</option>
        <option value="sample">sample</option>
        <option value="scientific_name">scientific_name</option>
        <option value="score">score</option>
        <option value="score_norm">score_norm</option>
        <option value="select">select</option>
        <option value="seq_ab_match">seq_ab_match</option>
        <option value="seq_a_single">seq_a_single</option>
        <option value="seq_a_mismatch">seq_a_mismatch</option>
        <option value="seq_a_deletion">seq_a_deletion</option>
        <option value="seq_a_insertion">seq_a_insertion</option>
        <option value="seq_b_single">seq_b_single</option>
        <option value="seq_b_mismatch">seq_b_mismatch</option>
        <option value="seq_b_deletion">seq_b_deletion</option>
        <option value="seq_b_insertion">seq_b_insertion</option>
        <option value="seq_length">seq_length</option>
        <option value="seq_length_ori">seq_length_ori</option>
        <option value="seq_rank">seq_rank</option>
        <option value="sminL">sminL</option>
        <option value="sminR">sminR</option>
        <option value="species">species</option>
        <option value="species_list">species_list</option>
        <option value="species_name">species_name</option>
        <option value="status">status</option>
        <option value="strand">strand</option>
        <option value="tail_quality">tail_quality</option>
        <option value="taxid">taxid</option>
    </xml>

    <xml name="inputtype">
        <option value="--genbank">genbank</option>
        <option value="--embl">embl</option>
        <option value="--sanger">sanger</option>
        <option value="--solexa">solexa</option>
        <option value="--ecopcr">ecopcr</option>
        <option value="--ecopcrdb">ecopcrdb</option>
        <option value="--fasta" selected="true">fasta</option>
    </xml>

    <xml name="sanitizer">
        <sanitizer invalid_char="test">
            <valid initial="default">
                <!--add value="&quot;"/-->
            </valid>
            <mapping initial="default">
                <add source="&gt;" target="\&gt;"/>
                <add source="&quot;" target="\&quot;"/>
            </mapping>
        </sanitizer>
    </xml>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1111/1755-0998.12428</citation>
        </citations>
    </xml>

</macros>