<tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>tags a set of sequences for PCR/sequencing errors identification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        @GUNZIP_INPUT@
        obiclean
        --without-progress-bar
        #if $distance
            -d '$distance'
        #end if
        #if $key
            -s '$key'
        #end if
        #if $ratio
            -r '$ratio'
        #end if
        ${head}
        @INPUT_FORMAT@
        @OUT_FORMAT@
        input 
        @GZIP_OUTPUT@
        >'$output'
        @GENERATE_GALAXY_JSON@
    ]]></command>
    <inputs>
        <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
        <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)"/>
        <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition"/>
        <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)"/>
        <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?"/>
        <expand macro="input_format_options_macro"/>
        <expand macro="out_format_macro"/>
    </inputs>
    <outputs>
        <data format="auto" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="output_obiannotate.fasta" />
            <param name="head" value="True"/>
            <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="output_obiannotate.fasta.gz" />
            <param name="key" value="merged_sample"/>
            <param name="ratio" value="0.05"/>
            <param name="head" value="False"/>
            <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

obijoinpairedend aims at joining the two reads of a paired-end library.

For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.

The program uses as input one or two sequences reads files.

If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.

@OBITOOLS_LINK@

        ]]>
    </help>
    <expand macro="citation"/>
    </tool>