--- a/jbrowse.xml	Mon May 04 17:21:38 2015 -0400
+++ b/jbrowse.xml	Thu Jun 18 12:10:51 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse" name="JBrowse" version="0.1">
+<tool id="jbrowse" name="JBrowse" version="0.3">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
@@ -8,25 +8,116 @@
   <version_command>python jbrowse.py --version</version_command>
   <command interpreter="python"><![CDATA[jbrowse.py
 $positional_1
-
-#set data_files = '" "'.join([ str($var.gff3) for $var in $data_tracks ])
-#set data_formats  = '" "'.join([ str($var.gff3.ext) for $var in $data_tracks ])
-#set data_labels = '" "'.join([ str($var.gff3_label) for $var in $data_tracks ])
-
---gff3 "$data_files"
---gff3_format "$data_formats"
---gff3_label "$data_labels"
-
+$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.annotation_label}"
+    category: "${track.category}"
+    options:
+        __unused__: "Not used...just to ensure options has at least one key"
+    #if str($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">
-        <param label="Annotation Data" help="in GFF, GFF3, or BED formats"
-            format="gff,gff3,bed" name="gff3" type="data"/>
-      <param label="Dataset Label" name="gff3_label" type="text"/>
+        <param label="Track Label" name="annotation_label" type="text"/>
+        <param label="Track Category" name="category" type="text" value="Default"
+            help="Organise your tracks into Categories for a nicer end-user experience"/>
+        <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</option>
+                <option value="wiggle">BigWig XY</option>
+                <option value="vcf">VCF SNPs</option>
+            </param>
+            <when value="blast">
+                <param label="BlastXML Track Data" format="blastxml" name="annotation" type="data"/>
+
+                <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="vcf">
+                <param label="SNPs" help="in VCF"
+                    format="vcf" name="annotation" type="data"/>
+            </when>
+            <when value="gene_calls">
+                <param label="Track Data" help="in GFF, GFF3, BED"
+                    format="gff,gff3,bed" name="annotation" type="data"/>
+
+                <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="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="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 variance 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>
+                        <option value="auto_global">Autoscale (global)</option>
+                        <option vlue="fixed">Specify Min/Max</option>
+                    </param>
+                    <when value="auto_local"></when>
+                    <when value="auto_global"></when>
+                    <when value="fixed">
+                        <param label="Track minimum" name="minimum"
+                            type="integer" value="0" />
+                        <param label="Track maximum" name="maximum"
+                            type="integer" value="100" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
     </repeat>
   </inputs>
   <outputs>