<tool id="stacks2_clonefilter" name="Stacks2: clone filter" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<description>Identify PCR clones</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_cmd"/>
    <command detect_errors="aggressive"><![CDATA[
@FASTQ_INPUT_FUNCTIONS@

trap ">&2 cat '$output_log'" err exit &&
mkdir stacks_inputs stacks_outputs &&

#set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
$link_command

clone_filter
#if $input_type.input_type_select == 'single':
    -f '$fwd_path'
#else
    -1 '$fwd_path'
    -2 '$rev_path'
#end if

-i $inputype

-o stacks_outputs
$capture
$input_type.barcode_encoding
#if $oligo_len_1
    --oligo_len_1 $oligo_len_1
#end if
#if $oligo_len_2
    --oligo_len_2 $oligo_len_2
#end if
$retain_oligo
## only supports fastq.gz output since the
## the program outputs empty files for fasta/fastq
-y gzfastq
@TEE_APPEND_LOG@

## move outputs such that Galaxy can find them
#if $capture:
    #if $input_type.input_type_select == "single"
        && mv stacks_outputs/*.discards.fq.gz '$discarded'
    #else
        && mv stacks_outputs/*.discards.1.fq.gz '$discarded_pair.forward'
        && mv stacks_outputs/*.discards.2.fq.gz '$discarded_pair.reverse'
    #end if
#end if
#if $input_type.input_type_select == "single"
    && mv stacks_outputs/*.fq.gz '$clean'
#else
    && mv stacks_outputs/*.1.fq.gz '$clean_pair.forward'
    && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse'
#end if
]]></command>
    <inputs>
        <expand macro="fastq_input_bc"/>
        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
        <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
        <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
        <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)"/>
        <expand macro="in_log"/>
    </inputs>
    <outputs>
        <expand macro="out_log"/>
        <expand macro="fastq_output_filter" format="fastqsanger.gz"/>
    </outputs>
    <tests>
        <!-- single end, defaults-->
        <test expect_num_outputs="2">
            <conditional name="input_type">
                <param name="input_type_select" value="single"/>
                <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
            </conditional>
            <param name="oligo_len_1" value="6"/>
            <param name="add_log" value="yes"/>
            <assert_command>
                <has_text text="--oligo_len_1 6"/>
                <not_has_text text="-D"/>
            </assert_command>
            <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
            <output name="clean" compare="diff"  ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
        </test>
        <!-- single end, alt BCencoding, capture-->
        <test expect_num_outputs="3">
            <conditional name="input_type">
                <param name="input_type_select" value="single"/>
                <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
                <param name="barcode_encoding" value="--index_null"/>
            </conditional>
            <param name="capture" value="true"/>
            <param name="oligo_len_1" value="6"/>
            <assert_command>
                <has_text text="--oligo_len_1 6"/>
                <has_text text="-D"/>
            </assert_command>
            <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output>
            <output name="clean" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
            <output name="discarded" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
        </test>
        <!-- paired end, defaults-->
        <test expect_num_outputs="4">
            <conditional name="input_type">
                <param name="input_type_select" value="paired"/>
                <param name="fqinputs">
                    <collection type="paired">
                        <element name="forward" value="clonefilter/R1_0001.1.fq.gz" ftype="fastqsanger.gz"/>
                        <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
                    </collection>
                </param>
            </conditional>
            <param name="oligo_len_1" value="6"/>
            <assert_command>
                <has_text text="--oligo_len_1 6"/>
                <not_has_text text="--oligo_len_2"/>
                <not_has_text text="-D"/>
            </assert_command>
            <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
            <output_collection name="clean_pair" type="paired" count="2"/>
        </test>
        <!-- paired end, non defaults -->
        <test expect_num_outputs="7">
            <conditional name="input_type">
                <param name="input_type_select" value="paired"/>
                <param name="fqinputs">
                    <collection type="paired">
                        <element name="forward" value="clonefilter/R1_0001.1.fq.gz" ftype="fastqsanger.gz"/>
                        <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
                    </collection>
                </param>
            </conditional>
            <param name="oligo_len_1" value="6"/>
            <param name="oligo_len_2" value="6"/>
            <param name="capture" value="true"/>
            <param name="retain_oligo" value="true"/>
            <assert_command>
                <has_text text="--oligo_len_1 6"/>
                <has_text text="--oligo_len_2 6"/>
                <has_text text="-D"/>
                <has_text text="--retain_oligo"/>
            </assert_command>
            <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
            <output_collection name="clean_pair" type="paired" count="2"/>
            <output_collection name="discarded_pair" type="paired" count="2"/>
        </test>
    </tests>
    <help>
<![CDATA[
.. class:: infomark

The clone_filter program is designed to identify PCR clones.

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