<tool id="tepid_discover" name="tepid-discover" version="@WRAPPER_VERSION@">
    <description>discover TE variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>tepid-discover --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    @LINK_CONC@
    tepid-discover
    -n '$split_bam.element_identifier'
    $deletions
    $insertions
    $strict
    #if $mask:
        --mask '$mask'
    #end if
    #if $discordant_bam:
        --discordant '$discordant_bam'
    #end if
    @PROC@
    @NAME@
    -c conc.bam
    -s '$split_bam'
    -t '$te_annotation_bed'
    -k
    $se_mode &&  ## The follwing is terrible, but from_work_dir cannot deal with variables
    #if not str($deletions)=="--deletions":
        mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
        mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
    #end if
    #if not str($insertions)=="--insertions":
        mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&
        mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&
    #end if
    cat tepid_discover_log_'$bowtie2_bam.element_identifier'.txt
    ]]></command>
    <inputs>
        <param name="bowtie2_bam" label="Alignment file (Bowtie2)" argument="--conc" type="data" format="bam"/>
        <param name="discordant_bam" label="Alignment file with discordant pairs" argument="--discordant" optional="true" type="data" format="bam"/>
        <param name="split_bam" label="Alignment file with split reads" argument="--split" type="data" format="bam"/>
        <param name="mask" type="select" optional="True" label="Select chromosomes that you would like to exclude" multiple="True">
            <options>
                <filter type="data_meta" ref="bowtie2_bam" key="reference_names" />
            </options>
        </param>
        <param name="te_annotation_bed" label="BED file with TE locations" argument="--te" type="data" format="bed"/>
        <param name="se_mode" argument="--se" type="boolean" truevalue="--se" falsevalue="" label="Run in single-end mode?"/>
        <param name="deletions" argument="--deletions" type="boolean" truevalue="--deletions" falsevalue="" label="Find deletions only?"/>
        <param name="insertions" argument="--insertions" type="boolean" truevalue="--insertions" falsevalue="" label="Find insertions only?"/>
        <param name="strict" argument="--strict" type="boolean" truevalue="--strict" falsevalue="" label="Report high-confidence variants only?"/>
    </inputs>
    <outputs>
        <data name="insertions_out" format="bed" label="tepid_discover insertions on ${on_string}"/>
        <data name="deletions_out" format="bed" label="tepid_discover deletions on ${on_string}"/>
        <data name="insertion_reads_out" format="txt" label="tepid_discover reads supporting insertions for ${on_string}"/>
        <data name="deletion_reads_out" format="txt" label="tepid_discover reads supporting deletions for ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="bowtie2_bam" value="conc.bam"/>
            <param name="split_bam" value="split.bam"/>
            <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
            <output name="insertions_out" file="insertions_test.bed"/>
            <output name="deletions_out" file="deletions_test.bed"/>
            <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
            <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
        </test>
    </tests>
    <help><![CDATA[
TEPID -- transposable element polymorphism identification

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -k, --keep            keep all intermediate files
  -d, --deletions       find deletions only
  -i, --insertions      find insertions only
  --strict              Report high-confidence variants only
  --mask MASK           Mask chromosomes in comma separated list or file
  -D DISCORDANT, --discordant DISCORDANT
                        Supply discordant reads bam file
  -p PROC, --proc PROC  number of processors
  -n NAME, --name NAME  sample name
  -c CONC, --conc CONC  bam file from bowtie2
  -s SPLIT, --split SPLIT
                        split reads bam file from yaha
  -t TE, --te TE        TE annotation bedfile
  --se                  Run in single-end mode
    ]]></help>
<expand macro="citations"/>
</tool>