<commit_before><tool id="jbrowse" name="JBrowse" version="0.2">
  <description>genome browser</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command>python jbrowse.py --version</version_command>
  <command interpreter="python"><![CDATA[jbrowse.py
$positional_1
$trackYaml

--jbrowse \${JBROWSE_SOURCE_DIR}
--outdir $default.files_path
> $default]]></command>
  <configfiles>
      <configfile name="trackYaml">
---
#for $track in $data_tracks:
  -
    file: ${track.data_format.annotation}
    ext: ${track.data_format.annotation.ext}
    label: "${track.data_format.annotation_label}"
    #if str($track.data_format.data_format_select) == "wiggle":
    options:
        type: ${track.data_format.xyplot}
        variance_band: ${track.data_format.var_band}
      #if str($track.data_format.scaling.scale_select) == "auto_local":
        autoscale: local
      #else if str($track.data_format.scaling.scale_select) == "auto_global":
        autoscale: global
      #else:
        min: ${track.data_format.scaling.minimum}
        max: ${track.data_format.scaling.maximum}
      #end if
    #else if str($track.data_format.data_format_select) == "pileup":
    options:
        auto_snp: ${track.data_format.auto_snp}
        bam_index: ${track.data_format.annotation.metadata.bam_index}
    #else if str($track.data_format.data_format_select) == "blastxml":
    options:
        parent: ${track.data_format.blast_parent}
        protein: ${track.data_format.is_protein}
        min_gap: ${track.data_format.min_gap}
    #end if
#end for
      </configfile>
  </configfiles>
  <inputs>
    <param label="Genome" name="positional_1" type="data" format="fasta"/>
    <repeat name="data_tracks" title="Annotation Track">
        <conditional name="data_format" label="Track Options">
            <param type="select" label="Track Type" name="data_format_select">
                <option value="gene_calls">GFF/GFF3/BED Featuers</option>
                <option value="pileup">BAM Pileups</option>
                <option value="blast">Blast XML Results</option>
                <option value="wiggle">BigWig XY Data</option>
            </param>
            <when value="blast">
                <param label="BlastXML Track Data" format="blastxml" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>

                <param label="Features used in Blast Search" help="in GFF3. This is required so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file."
                    format="gff3" name="blast_parent" type="data"/>

                <param label="Minimum Gap Size" help="before a new match_part feature is created" name="min_gap"
                    type="integer" value="10" min="2" />
                <param label="Is this a protein blast search?"
                    type="boolean" name="is_protein" truevalue="true" falsevalue="false" />
            </when>
            <when value="gene_calls">
                <param label="Track Data" help="in GFF, GFF3, BED"
                    format="gff,gff3,bed" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>
            </when>
            <when value="pileup">
                <param label="Track Data" help="in BAM"
                    format="bam" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>
                <param label="Autogenerate SNP Track" help="Not recommended for deep coverage BAM files"
                    type="boolean" name="auto_snp" truevalue="true" falsevalue="false" />
            </when>
            <when value="wiggle">
                <param label="Track Data" help="in BigWig"
                    format="bigwig" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>
                <param label="Use XYPlot" help="instead of continuous coloured band"
                    type="boolean" name="xyplot" truevalue="JBrowse/View/Track/Wiggle/XYPlot"
                    falsevalue="JBrowse/View/Track/Wiggle/Density" />
                <param label="Show variane band" help="Only for XYPlots"
                    type="boolean" name="var_band" truevalue="true"
                    falsevalue="false" />

                <conditional name="scaling" label="Scaling">
                    <param type="select" label="Track Scaling" name="scale_select">
                        <option value="auto_local">Autoscale (local)</option><commit_msg>Support for match/match_part<commit_after><tool id="jbrowse" name="JBrowse" version="0.2">
  <description>genome browser</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command>python jbrowse.py --version</version_command>
  <command interpreter="python"><![CDATA[jbrowse.py
$positional_1
$trackYaml

--jbrowse \${JBROWSE_SOURCE_DIR}
--outdir $default.files_path
> $default]]></command>
  <configfiles>
      <configfile name="trackYaml">
---
#for $track in $data_tracks:
  -
    file: ${track.data_format.annotation}
    ext: ${track.data_format.annotation.ext}
    label: "${track.data_format.annotation_label}"
    options:
        __unused__: "Not used...just to ensure options has at least one key"
    #if str($track.data_format.data_format_select) == "wiggle":
        type: ${track.data_format.xyplot}
        variance_band: ${track.data_format.var_band}
      #if str($track.data_format.scaling.scale_select) == "auto_local":
        autoscale: local
      #else if str($track.data_format.scaling.scale_select) == "auto_global":
        autoscale: global
      #else:
        min: ${track.data_format.scaling.minimum}
        max: ${track.data_format.scaling.maximum}
      #end if
    #else if str($track.data_format.data_format_select) == "pileup":
        auto_snp: ${track.data_format.auto_snp}
        bam_index: ${track.data_format.annotation.metadata.bam_index}
    #else if str($track.data_format.data_format_select) == "blast":
        parent: ${track.data_format.blast_parent}
        protein: ${track.data_format.is_protein}
        min_gap: ${track.data_format.min_gap}
        match: true
    #else if str($track.data_format.data_format_select) == "gene_calls":
        match: ${track.data_format.match_part}
    #end if
#end for
      </configfile>
  </configfiles>
  <inputs>
    <param label="Genome" name="positional_1" type="data" format="fasta"/>
    <repeat name="data_tracks" title="Annotation Track">
        <conditional name="data_format" label="Track Options">
            <param type="select" label="Track Type" name="data_format_select">
                <option value="gene_calls">GFF/GFF3/BED Featuers</option>
                <option value="pileup">BAM Pileups</option>
                <option value="blast">Blast XML Results</option>
                <option value="wiggle">BigWig XY Data</option>
            </param>
            <when value="blast">
                <param label="BlastXML Track Data" format="blastxml" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>

                <param label="Features used in Blast Search" help="in GFF3. This is required so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file."
                    format="gff3" name="blast_parent" type="data"/>

                <param label="Minimum Gap Size" help="before a new match_part feature is created" name="min_gap"
                    type="integer" value="10" min="2" />
                <param label="Is this a protein blast search?"
                    type="boolean" name="is_protein" truevalue="true" falsevalue="false" />
            </when>
            <when value="gene_calls">
                <param label="Track Data" help="in GFF, GFF3, BED"
                    format="gff,gff3,bed" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>

                <param label="This is match/match_part data"
                    type="boolean" name="match_part" truevalue="true" falsevalue="false" />
            </when>
            <when value="pileup">
                <param label="Track Data" help="in BAM"
                    format="bam" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>
                <param label="Autogenerate SNP Track" help="Not recommended for deep coverage BAM files"
                    type="boolean" name="auto_snp" truevalue="true" falsevalue="false" />
            </when>
            <when value="wiggle">
                <param label="Track Data" help="in BigWig"
                    format="bigwig" name="annotation" type="data"/>
                <param label="Track Label" name="annotation_label" type="text"/>
                <param label="Use XYPlot" help="instead of continuous coloured band"
                    type="boolean" name="xyplot" truevalue="JBrowse/View/Track/Wiggle/XYPlot"
                    falsevalue="JBrowse/View/Track/Wiggle/Density" />
                <param label="Show variane band" help="Only for XYPlots"
                    type="boolean" name="var_band" truevalue="true"
                    falsevalue="false" />

                <conditional name="scaling" label="Scaling">
                    <param type="select" label="Track Scaling" name="scale_select">
                        <option value="auto_local">Autoscale (local)</option>
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