<tool profile="16.07" id="mothur_chop_seqs" name="Chop.seqs" version="@WRAPPER_VERSION@.0">
    <description>Trim sequences to a specified length</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&
ln -s '$count' count.dat &&

echo 'chop.seqs(
    fasta=fasta.dat,
    numbases=$numbases,
    keep=$keep,
    countgaps=$countgaps,
    short=$short,
    #if $name:
        name=name.dat,
    #end if
    #if $group:
        group=group.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
        <param argument="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
        <param argument="keep" type="select" label="keep - Part of the sequence to keep">
            <option value="front">front</option>
            <option value="back">back</option>
        </param>
        <param argument="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
        <param argument="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
        <param argument="name" type="data" format="mothur.names" optional="true"  label="name file"/>
        <param argument="group" type="data" format="mothur.groups" optional="true" label="group file"/>
        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.chop.fasta" label="${tool.name} on ${on_string}: chop.fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.

.. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs

v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0

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