<tool id="ab1_fastq_converter" name="ab1 to FASTQ converter" version="@VERSION@">
    <description></description>
    <macros>
        <import>ab1fastq_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.28.0">bioconductor-sangerseqr</requirement>
        <requirement type="package" version="@VERSION@">bioconductor-crisprvariants</requirement>
    </requirements>
    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", sangerseqR version" $(R --vanilla --slave -e "library(sangerseqR); cat(sessionInfo()\\$otherPkgs\$sangerseqR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", CrispRVariants version" $(R --vanilla --slave -e "library(CrispRVariants); cat(sessionInfo()\\$otherPkgs\$CrispRVariants\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
         '$__tool_directory__/ab1_fastq.R'
         '$input'
         '${input.display_name}'
         #if $tr.trim=='true'
           'TRUE'
           '$tr.cutoff'
           '$tr.minseq'
           '$tr.offset'
         #else
           'FALSE'
           '0.05'
           '20'
           '33'
         #end if
         '$output'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="ab1" label="Input ab1 file"/>
        <conditional name="tr">
            <param name="trim" type="select" label="Do you want trim ends according to quality scores ?">
                <option value="false" selected="true">No, use full sequences.</option>
                <option value="true">Yes, trim low-quality ends.</option>
            </param>
            <when value="false">
            </when>
            <when value="true">
                <param name="cutoff" type="float" value="0.05" min="0" max="1" label="Probability cutoff you want to use to trim"/>
                <param name="minseq" type="integer" value="20" min="0" label="Minimum sequence length to allow the trim"/>
                <param name="offset" type="float" value="33" min="0" label="Phred offset for quality scores"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" from_work_dir="output.fastq" format="fastq" label="${input.display_name}.fastq"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test_file.AB1"/>
            <param name="trim" value="false"/>
            <output name="output" value="out_file.fastq"/>
        </test>
    </tests>
    <help><![CDATA[
============================
Convert ab1 files into FASTQ
============================

.ab1, .AB1 or .abi files are common sanger sequencing outputs, this tool permits you to convert it into fastq so it can be used into many galaxy tools.

This tool can also trim ends of your sequence based on the quality statistics.
    ]]></help>
    <citations>
        <citation type="doi">10.1038/nbt.3628</citation>
        <citation type="doi">10.5061/dryad.b331s</citation>
    </citations>
</tool>