<tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0">
    <requirements>
        <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #for $inputsection in $inputfiles
            #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
            sed -i.bak -e "s|$path|\$PWD/$path|g" '$igv_session' &&
            ln -fs '$inputsection.input' '$path' &&
            #if $inputsection.input.is_of_type('bam')
                ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
            #end if
        #end for
        ln -fs $igv_session igv_session.xml &&
        cat '$load_session' > load_session.txt &&
        echo snapshotDirectory "\$PWD" >> load_session.txt &&
        cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
        ## gives the cluster a bit of time to actually create the symlinks ... ughs
        sleep 10s &&
        python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
        cp '$igv_session' '$igv_session_out' &&
        zip screenshots.zip *.png &&
        cp screenshots.zip '$screenshots_out'
    ]]></command>
    <configfiles>
        <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
    <Resources>
        #for $inputsection in $inputfiles
            #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
            #set $coverage_id="%s_coverage" % $path
        <Resource path="$path"/>
        #end for
    </Resources>
    #for $inputsection in $inputfiles
        #if $inputsection.input.is_of_type('bam')
            #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
            #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
            <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
            ## First track is the coverage
            <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
                <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
            </Track>
            ## Second track is the actual BAM alignment file
            <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" sortable="true" visible="true">
                <RenderOptions colorByTag="$inputsection.color_by_tag" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/>
            </Track>
            </Panel>
        #end if
    #end for
    <Panel height="186" name="FeaturePanel" width="$width">
        <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>
        <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;817.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="${genome}_genes" name="Gene" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/>
        </Track>
        #for $inputsection in $inputfiles
            #if not $inputsection.input.is_of_type('bam')
                #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
                #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
                <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
             #end if
        #end for
    </Panel>
    <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
</Session>
        ]]></configfile>
        <configfile name="load_session">
load igv_session.xml
preference SAM.SHOW_SOFT_CLIPPED str($show_softclippped)
        </configfile>
        <configfile name="exit_session">
exit
        </configfile>
    </configfiles>
    <inputs>
        <repeat name="inputfiles" min="1" title="Add tracks">
            <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file">
                    <validator type="unspecified_build" />
            </param>
            <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/>
            <param name="section_height" type="integer" value="300" label="Height for this track"/>
            <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read">
                <sanitizer invalid_char="">
                    <valid initial="string.letters,string.digits"><add value="_" /> </valid>
                </sanitizer>
            </param>
        </repeat>
        <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
        <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
        <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/>
        <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
    </inputs>
    <outputs>
        <data name="igv_session_out" format="xml"/>
        <data name="screenshots_out" format="zip"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>