<tool id="ribopicker" name="riboPicker" version="1.0.0">
    <description>Easy identification and removal of rRNA-like sequences.</description>
    <version_command>ribopicker.pl -version | awk '{print $3}'</version_command>
    <command interpreter="bash">ribopicker.sh
        -id 'galaxy'
    #if $identity_threshold:
        -i $identity_threshold
    #end if
    #if $coverage_threshold:
        -c $coverage_threshold
    #end if
    #if $length_threshold:
        -l $length_threshold
    #end if
    #if $read_chunk_size:
        -S $read_chunk_size
    #end if
    #if $z_best_value:
        -z $z_best_value
    #end if
    #if $align_score_threshold:
        -T $align_score_threshold
    #end if
     -f $input
    </command>
    <inputs>
        <param name="input" type="data" format="fastq,fasta" label="from"
            help="Input file in FASTA or FASTQ format that contains the query
            sequences."/>
        <param name="dbs" type="select" label="Reference Database">
          <options from_data_table="ribopicker_dbs">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No reference databases are available" />
          </options>
        </param>
    <param name="identity_threshold" type="integer" value="" size="3"
        label="Alignment Identity Threshold" optional="True" help="Alignment
        identity threshold in percentage (integer from 1-100 without %) used to
        define matching sequences as similar. The identity is calculated for the
        part of the query sequence that is aligned to a reference sequence. For
        example, a query sequence of 100 bp that aligns to a reference sequence
        over the first 50 bp with 40 matching positions has an identity value of
        80%." >
        <validator type="in_range" message="(1-100)" min="1" max="100"/>
    </param>
    <param name="coverage_threshold" type="integer" value="" size="3"
        label="Alignment Coverage Threshold" optional="True" help="Alignment
        coverage threshold in percentage (integer from 1-100 without %) used to
        define matching sequences as similar. The coverage is calculated for the
        part of the query sequence that is aligned to a reference sequence. For
        example, a query sequence of 100 bp that aligns to a reference sequence
        over the first 50 bp with 40 matching positions has an coverage value of
        50%." >
        <validator type="in_range" message="(1-100)" min="1" max="100"/>
    </param>
    <param name="length_threshold" type="integer" value="" size="5"
        label="Alignment Length Threshold" optional="True" help="Alignment
        length threshold used to define matching sequences as similar. For
        example, a query sequence of 100 bp that aligns to a reference sequence
        over the first 50 bp with 40 matching positions has an alignment length
        of 50." >
        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
    </param>
    <param name="read_chunk_size" type="integer" value="" size="9"
        label="Chunk size of reads in bp for BWA-SW" optional="True" help="Chunk
        size of reads in bp as used by BWA-SW (default: 10000000)" >
        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
    </param>
    <param name="z_best_value" type="integer" value="" size="5"
        label="Z-best value for BWA-SW" optional="True" help="Z-best value as
        used by BWA-SW (default: 1)">
        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
    </param>
    <param name="align_score_threshold" type="integer" value="" size="5"
        label="Alignment score threshold for BWA-SW" optional="True"
        help="Alignment score threshold as used by BWA-SW (default: 30)" >
        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
    </param>
    </inputs>
    <outputs>
        <data name="rrna" format="fasta" from_work_dir="galaxy_rrna.txt" label="rRNA" />
        <data name="nonrrna" format="fasta" from_work_dir="galaxy_nonrrna.txt" label="Non-rRNA" />
    </outputs>
    <!--
    Usage:
        ribopicker [options] -f <file> -dbs <list> ...
    Options:
        -T <integer>
            Alignment score threshold as used by BWA-SW (default: 30).
-->
<help>
**What it does**

The riboPicker tool can be used to automatically identify and efficiently
remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
</help>
</tool>