<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Sorts and matches sequence records with matching coordinates across files</description>
    <macros>
        <import>presto_macros.xml</import>
	</macros>
    <expand macro="bio_tools"/>

	<expand macro="requirements"/>

    <version_command>PairSeq.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$r1_in' r1.fastq &&
        ln -s '$r2_in' r2.fastq &&
        PairSeq.py
          -1 r1.fastq
          -2 r2.fastq
          --coord $coord
          #if $r1_annotations
          --1f $r1_annotations
          #end if
          #if $r2_annotations
          --2f $r2_annotations
          #end if
		  $failed
          --outdir=.
          --outname=tmp
    ]]></command>
    <inputs>
        <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/>
        <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ/FASTA file."/>
        <param argument="--1f" name="r1_annotations" type="text" optional="true" label="Annotation(s) to copy from R1 to R2." help="Multiple annotation must be space-separated.">
            <expand macro="text-regex-validator"/>
        </param>
        <param argument="--2f" name="r2_annotations" type="text" optional="true" label="Annotation(s) to copy from R2 to R1." help="Multiple annotation must be space-separated.">
            <expand macro="text-regex-validator"/>
        </param>
        <expand macro="presto-coord-param"/>
        <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" />
    </inputs>
    <outputs>
        <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq" label="${tool.name} on ${on_string}: Paired R1"/>
        <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq" label="${tool.name} on ${on_string}: Paired R2"/>
        <!-- only give these 2 outputs if input failed_fastq=True-->
        <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq" label="${tool.name} on ${on_string}: Unpaired R1">
            <filter>failed</filter>
        </data>
        <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq" label="${tool.name} on ${on_string}: Unpaired R2">
            <filter>failed</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
            <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
            <param name="r2_annotations" value="BARCODE"/>
            <param name="coord" value="illumina"/>
            <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
            <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
        </test>
        <test expect_num_outputs="4">
            <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
            <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
            <param name="r2_annotations" value="BARCODE"/>
            <param name="coord" value="illumina"/>
            <param name="failed" value="true"/>
            <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
            <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
            <output name="r1_fail_out">
                <assert_contents>
                    <has_text text="@"/>
                </assert_contents>
            </output>
            <output name="r2_fail_out">
                <assert_contents>
                    <has_text text="@"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Sorts and matches sequence records with matching coordinates across files.

See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.

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