changeset 7:326a3db8d9d1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
author iuc
date Fri, 17 Apr 2020 11:57:44 -0400
parents 5cec5fb749f0
children 4ac4e7083b7e
files macros.xml pyGenomeTracks.xml test-data/dm3_genes_withrgbandscore.bed.gz test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/test13.ini test-data/test14.ini test-data/test15.ini test-data/test3.ini test-data/test6.ini test-data/test7.ini test-data/test_arrowhead_zoom.png test-data/test_gtf_bed4.png test-data/test_gtf_flybase_param.png test-data/test_link2.png test-data/test_narrowPeak.png test-data/test_scale_bar.png test-data/test_tssarrow.png test-data/test_ucsc_param.png test-data/testpyGT.sh
diffstat 20 files changed, 1202 insertions(+), 686 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Feb 11 10:20:24 2020 -0500
+++ b/macros.xml	Fri Apr 17 11:57:44 2020 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">3.2.1</token>
+    <token name="@WRAPPER_VERSION@">3.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
@@ -15,159 +15,6 @@
             <yield />
         </citations>
     </xml>
-
-    <xml name="colormap">
-        <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
-            <option value="RdYlBu">RdYlBu</option>
-            <option value="Accent">Accent</option>
-            <option value="Spectral">Spectral</option>
-            <option value="Set1">Set1</option>
-            <option value="Set2">Set2</option>
-            <option value="Set3">Set3</option>
-            <option value="Dark2">Dark2</option>
-            <option value="Reds">Reds</option>
-            <option value="Oranges">Oranges</option>
-            <option value="Greens">Greens</option>
-            <option value="Blues">Blues</option>
-            <option value="Greys">Greys</option>
-            <option value="Purples">Purples</option>
-            <option value="Paired">Paired</option>
-            <option value="Pastel1">Pastel1</option>
-            <option value="Pastel2">Pastel2</option>
-            <option value="spring">spring</option>
-            <option value="summer">summer</option>
-            <option value="autumn">autumn</option>
-            <option value="winter">winter</option>
-            <option value="hot">hot</option>
-            <option value="coolwarm">coolwarm</option>
-            <option value="cool">cool</option>
-            <option value="seismic">seismic</option>
-            <option value="terrain">terrain</option>
-            <option value="ocean">ocean</option>
-            <option value="rainbow">rainbow</option>
-            <option value="bone">bone</option>
-            <option value="flag">flag</option>
-            <option value="prism">prism</option>
-            <option value="cubehelix">cubehelix</option>
-            <option value="binary">binary</option>
-            <option value="pink">pink</option>
-            <option value="gray">gray</option>
-            <option value="copper">copper</option>
-            <option value="BrBG">BrBG</option>
-            <option value="BuGn">BuGn</option>
-            <option value="BuPu">BuPu</option>
-            <option value="GnBu">GnBu</option>
-            <option value="OrRd">OrRd</option>
-            <option value="PiYG">PiYG</option>
-            <option value="PRGn">PRGn</option>
-            <option value="PuOr">PuOr</option>
-            <option value="PuRd">PuRd</option>
-            <option value="PuBu">PuBu</option>
-            <option value="RdBu">RdBu</option>
-            <option value="RdGy">RdGy</option>
-            <option value="RdPu">RdPu</option>
-            <option value="YlGn">YlGn</option>
-            <option value="PuBuGn">PuBuGn</option>
-            <option value="RdYlGn">RdYlGn</option>
-            <option value="YlGnBu">YlGnBu</option>
-            <option value="YlOrBr">YlOrBr</option>
-            <option value="YlOrRd">YlOrRd</option>
-            <option value="gist_gray">gist_gray</option>
-            <option value="gist_stern">gist_stern</option>
-            <option value="gist_earth">gist_earth</option>
-            <option value="gist_yarg">gist_yarg</option>
-            <option value="gist_ncar">gist_ncar</option>
-            <option value="gist_rainbow">gist_rainbow</option>
-            <option value="gist_heat">gist_heat</option>
-            <option value="gnuplot">gnuplot</option>
-            <option value="gnuplot2">gnuplot2</option>
-            <option value="CMRmap">CMRmap</option>
-            <option value="bwr">bwr</option>
-            <option value="hsv">hsv</option>
-            <option value="brg">brg</option>
-            <option value="jet">jet</option>
-            <option value="afmhot">afmhot</option>
-            <option value="Accent_r">Accent reversed</option>
-            <option value="Spectral_r">Spectral reversed</option>
-            <option value="Set1_r">Set1 reversed</option>
-            <option value="Set2_r">Set2 reversed</option>
-            <option value="Set3_r">Set3 reversed</option>
-            <option value="Dark2_r">Dark2 reversed</option>
-            <option value="Reds_r">Reds reversed</option>
-            <option value="Oranges_r">Oranges reversed</option>
-            <option value="Greens_r">Greens reversed</option>
-            <option value="Blues_r">Blues reversed</option>
-            <option value="Greys_r">Greys reversed</option>
-            <option value="Purples_r">Purples reversed</option>
-            <option value="Paired_r">Paired reversed</option>
-            <option value="Pastel1_r">Pastel1 reversed</option>
-            <option value="Pastel2_r">Pastel2 reversed</option>
-            <option value="spring_r">spring reversed</option>
-            <option value="summer_r">summer reversed</option>
-            <option value="autumn_r">autumn reversed</option>
-            <option value="winter_r">winter reversed</option>
-            <option value="hot_r">hot reversed</option>
-            <option value="coolwarm_r">coolwarm reversed</option>
-            <option value="cool_r">cool reversed</option>
-            <option value="seismic_r">seismic reversed</option>
-            <option value="terrain_r">terrain reversed</option>
-            <option value="ocean_r">ocean reversed</option>
-            <option value="rainbow_r">rainbow reversed</option>
-            <option value="bone_r">bone reversed</option>
-            <option value="flag_r">flag reversed</option>
-            <option value="prism_r">prism reversed</option>
-            <option value="cubehelix_r">cubehelix reversed</option>
-            <option value="binary_r">binary reversed</option>
-            <option value="pink_r">pink reversed</option>
-            <option value="gray_r">gray reversed</option>
-            <option value="copper_r">copper reversed</option>
-            <option value="BrBG_r">BrBG reversed</option>
-            <option value="BuGn_r">BuGn reversed</option>
-            <option value="BuPu_r">BuPu reversed</option>
-            <option value="GnBu_r">GnBu reversed</option>
-            <option value="OrRd_r">OrRd reversed</option>
-            <option value="PiYG_r">PiYG reversed</option>
-            <option value="PRGn_r">PRGn reversed</option>
-            <option value="PuOr_r">PuOr reversed</option>
-            <option value="PuRd_r">PuRd reversed</option>
-            <option value="PuBu_r">PuBu reversed</option>
-            <option value="RdBu_r">RdBu reversed</option>
-            <option value="RdGy_r">RdGy reversed</option>
-            <option value="RdPu_r">RdPu reversed</option>
-            <option value="YlGn_r">YlGn reversed</option>
-            <option value="PuBuGn_r">PuBuGn reversed</option>
-            <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
-            <option value="RdYlGn_r">RdYlGn reversed</option>
-            <option value="YlGnBu_r">YlGnBu reversed</option>
-            <option value="YlOrBr_r">YlOrBr reversed</option>
-            <option value="YlOrRd_r">YlOrRd reversed</option>
-            <option value="gist_gray_r">gist_gray reversed</option>
-            <option value="gist_stern_r">gist_stern reversed</option>
-            <option value="gist_earth_r">gist_earth reversed</option>
-            <option value="gist_yarg_r">gist_yarg reversed</option>
-            <option value="gist_ncar_r">gist_ncar reversed</option>
-            <option value="gist_rainbow_r">gist_rainbow reversed</option>
-            <option value="gist_heat_r">gist_heat reversed</option>
-            <option value="gnuplot_r">gnuplot reversed</option>
-            <option value="gnuplot2_r">gnuplot2 reversed</option>
-            <option value="CMRmap_r">CMRmap reversed</option>
-            <option value="bwr_r">bwr reversed</option>
-            <option value="hsv_r">hsv reversed</option>
-            <option value="brg_r">brg reversed</option>
-            <option value="jet_r">jet reversed</option>
-            <option value="afmhot_r">afmhot reversed</option>
-        </param>
-    </xml>
-
-    <xml name="region">
-        <param argument="--region" type="text" label="Region of the genome to limit the operation"
-            help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
-    </xml>
-
-    <xml name="matrix_h5_cooler_multiple_macro">
-        <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"
-            label="Matricies to compute on" multiple="true"/>
-    </xml>
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -184,31 +31,36 @@
 .. _help site: https://github.com/deeptools/pyGenomeTracks
 
     </token>
-
+    <!-- all input files-->
+    <xml name="matrix_h5_cooler_multiple_macro">
+        <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"
+            label="Matricies to plot" multiple="true"/>
+    </xml>
     <xml name="track_input_bed_macro">
-        <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple="True"/>
+        <param name="track_input_bed" type="data" format="bed" label="Track file(s) bed format" multiple="True"/>
     </xml>
     <xml name="track_input_bed_gtf_macro">
-        <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple="True"/>
+        <param name="track_input_bed" type="data" format="bed,gtf" label="Track file(s) bed or gtf format" multiple="True"/>
     </xml>
     <xml name="track_input_narrow_peak_macro">
-        <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple="True"/>
+        <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file(s) encodepeak or bed format" multiple="True"/>
     </xml>
     <xml name="track_input_bed_single_macro">
         <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
     </xml>
     <xml name="track_input_bedgraph_macro">
-        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple="True"/>
+        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/>
     </xml>
     <xml name="track_input_bigwig_macro">
-        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple="True"/>
+        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file(s) bigwig format" multiple="True"/>
     </xml>
     <xml name="track_input_bedgraph_matrix_macro">
-        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple="True"/>
+        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/>
     </xml>
     <xml name="track_input_link_macro">
-        <param name="track_input_link" type="data" format="bed,interval" label="Track file for links" multiple="False"/>
+        <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/>
     </xml>
+    <!-- Common to nearly all tracks: -->
     <xml name="plot_title">
         <param name="title" type="text" optional="true" label="Plot title" multiple="True"/>
     </xml>
@@ -220,162 +72,18 @@
         <param name="invert_orientation" type="boolean" truevalue="true" falsevalue="false" checked="false"
                label="Invert the track" />
     </xml>
-    <xml name="color_bed_macro">
-        <conditional name="color_bed">
-            <param name="color_bed_select" type="select" label="Use color:">
-                <option value="manually" selected="True">manually</option>
-                <option value="bed_rgb">From the 9th field</option>
-                <option value="colormap">From the 5th field (score)</option>
-            </param>
-            <when value="manually">
-                <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
-            </when>
-            <when value="bed_rgb" />
-            <when value="colormap">
-              <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
-                <option value="RdYlBu">RdYlBu</option>
-                <option value="Accent">Accent</option>
-                <option value="Spectral">Spectral</option>
-                <option value="Set1">Set1</option>
-                <option value="Set2">Set2</option>
-                <option value="Set3">Set3</option>
-                <option value="Dark2">Dark2</option>
-                <option value="Reds">Reds</option>
-                <option value="Oranges">Oranges</option>
-                <option value="Greens">Greens</option>
-                <option value="Blues">Blues</option>
-                <option value="Greys">Greys</option>
-                <option value="Purples">Purples</option>
-                <option value="Paired">Paired</option>
-                <option value="Pastel1">Pastel1</option>
-                <option value="Pastel2">Pastel2</option>
-                <option value="spring">spring</option>
-                <option value="summer">summer</option>
-                <option value="autumn">autumn</option>
-                <option value="winter">winter</option>
-                <option value="hot">hot</option>
-                <option value="coolwarm">coolwarm</option>
-                <option value="cool">cool</option>
-                <option value="seismic">seismic</option>
-                <option value="terrain">terrain</option>
-                <option value="ocean">ocean</option>
-                <option value="rainbow">rainbow</option>
-                <option value="bone">bone</option>
-                <option value="flag">flag</option>
-                <option value="prism">prism</option>
-                <option value="cubehelix">cubehelix</option>
-                <option value="binary">binary</option>
-                <option value="pink">pink</option>
-                <option value="gray">gray</option>
-                <option value="copper">copper</option>
-                <option value="BrBG">BrBG</option>
-                <option value="BuGn">BuGn</option>
-                <option value="BuPu">BuPu</option>
-                <option value="GnBu">GnBu</option>
-                <option value="OrRd">OrRd</option>
-                <option value="PiYG">PiYG</option>
-                <option value="PRGn">PRGn</option>
-                <option value="PuOr">PuOr</option>
-                <option value="PuRd">PuRd</option>
-                <option value="PuBu">PuBu</option>
-                <option value="RdBu">RdBu</option>
-                <option value="RdGy">RdGy</option>
-                <option value="RdPu">RdPu</option>
-                <option value="YlGn">YlGn</option>
-                <option value="PuBuGn">PuBuGn</option>
-                <option value="RdYlGn">RdYlGn</option>
-                <option value="YlGnBu">YlGnBu</option>
-                <option value="YlOrBr">YlOrBr</option>
-                <option value="YlOrRd">YlOrRd</option>
-                <option value="gist_gray">gist_gray</option>
-                <option value="gist_stern">gist_stern</option>
-                <option value="gist_earth">gist_earth</option>
-                <option value="gist_yarg">gist_yarg</option>
-                <option value="gist_ncar">gist_ncar</option>
-                <option value="gist_rainbow">gist_rainbow</option>
-                <option value="gist_heat">gist_heat</option>
-                <option value="gnuplot">gnuplot</option>
-                <option value="gnuplot2">gnuplot2</option>
-                <option value="CMRmap">CMRmap</option>
-                <option value="bwr">bwr</option>
-                <option value="hsv">hsv</option>
-                <option value="brg">brg</option>
-                <option value="jet">jet</option>
-                <option value="afmhot">afmhot</option>
-                <option value="Accent_r">Accent reversed</option>
-                <option value="Spectral_r">Spectral reversed</option>
-                <option value="Set1_r">Set1 reversed</option>
-                <option value="Set2_r">Set2 reversed</option>
-                <option value="Set3_r">Set3 reversed</option>
-                <option value="Dark2_r">Dark2 reversed</option>
-                <option value="Reds_r">Reds reversed</option>
-                <option value="Oranges_r">Oranges reversed</option>
-                <option value="Greens_r">Greens reversed</option>
-                <option value="Blues_r">Blues reversed</option>
-                <option value="Greys_r">Greys reversed</option>
-                <option value="Purples_r">Purples reversed</option>
-                <option value="Paired_r">Paired reversed</option>
-                <option value="Pastel1_r">Pastel1 reversed</option>
-                <option value="Pastel2_r">Pastel2 reversed</option>
-                <option value="spring_r">spring reversed</option>
-                <option value="summer_r">summer reversed</option>
-                <option value="autumn_r">autumn reversed</option>
-                <option value="winter_r">winter reversed</option>
-                <option value="hot_r">hot reversed</option>
-                <option value="coolwarm_r">coolwarm reversed</option>
-                <option value="cool_r">cool reversed</option>
-                <option value="seismic_r">seismic reversed</option>
-                <option value="terrain_r">terrain reversed</option>
-                <option value="ocean_r">ocean reversed</option>
-                <option value="rainbow_r">rainbow reversed</option>
-                <option value="bone_r">bone reversed</option>
-                <option value="flag_r">flag reversed</option>
-                <option value="prism_r">prism reversed</option>
-                <option value="cubehelix_r">cubehelix reversed</option>
-                <option value="binary_r">binary reversed</option>
-                <option value="pink_r">pink reversed</option>
-                <option value="gray_r">gray reversed</option>
-                <option value="copper_r">copper reversed</option>
-                <option value="BrBG_r">BrBG reversed</option>
-                <option value="BuGn_r">BuGn reversed</option>
-                <option value="BuPu_r">BuPu reversed</option>
-                <option value="GnBu_r">GnBu reversed</option>
-                <option value="OrRd_r">OrRd reversed</option>
-                <option value="PiYG_r">PiYG reversed</option>
-                <option value="PRGn_r">PRGn reversed</option>
-                <option value="PuOr_r">PuOr reversed</option>
-                <option value="PuRd_r">PuRd reversed</option>
-                <option value="PuBu_r">PuBu reversed</option>
-                <option value="RdBu_r">RdBu reversed</option>
-                <option value="RdGy_r">RdGy reversed</option>
-                <option value="RdPu_r">RdPu reversed</option>
-                <option value="YlGn_r">YlGn reversed</option>
-                <option value="PuBuGn_r">PuBuGn reversed</option>
-                <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
-                <option value="RdYlGn_r">RdYlGn reversed</option>
-                <option value="YlGnBu_r">YlGnBu reversed</option>
-                <option value="YlOrBr_r">YlOrBr reversed</option>
-                <option value="YlOrRd_r">YlOrRd reversed</option>
-                <option value="gist_gray_r">gist_gray reversed</option>
-                <option value="gist_stern_r">gist_stern reversed</option>
-                <option value="gist_earth_r">gist_earth reversed</option>
-                <option value="gist_yarg_r">gist_yarg reversed</option>
-                <option value="gist_ncar_r">gist_ncar reversed</option>
-                <option value="gist_rainbow_r">gist_rainbow reversed</option>
-                <option value="gist_heat_r">gist_heat reversed</option>
-                <option value="gnuplot_r">gnuplot reversed</option>
-                <option value="gnuplot2_r">gnuplot2 reversed</option>
-                <option value="CMRmap_r">CMRmap reversed</option>
-                <option value="bwr_r">bwr reversed</option>
-                <option value="hsv_r">hsv reversed</option>
-                <option value="brg_r">brg reversed</option>
-                <option value="jet_r">jet reversed</option>
-                <option value="afmhot_r">afmhot reversed</option>
-              </param>
-            </when>
-        </conditional>
-        <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
+    <xml name="overlay_macro">
+        <param name="overlay_select" type="select" label="Overlay this track with the previous one:">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+            <option value="share-y">Yes and keep same y axis</option>
+        </param>
     </xml>
+    <xml name="minmax_macro">
+        <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
+        <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
+    </xml>
+    <!-- More specific but still present twice:-->
     <xml name="color_coverage_macro">
         <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
         <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
@@ -390,13 +98,6 @@
             </when>
         </conditional>
     </xml>
-    <xml name="overlay_macro">
-        <param name="overlay_select" type="select" label="Overlay this track with the previous one:">
-            <option value="no" selected="True">No</option>
-            <option value="yes">Yes</option>
-            <option value="share-y">Yes and keep same y axis</option>
-        </param>
-    </xml>
     <xml name="type_coverage_macro">
         <conditional name="type_conditional">
             <param name="type_selector" type="select" label="Choose style of the plot.">
@@ -413,46 +114,48 @@
             <when value="fill_option" />
         </conditional>
     </xml>
-    <xml name="minmax_macro">
-        <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
-        <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
-    </xml>
-    <xml name="reading_bw_macro">
-        <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
-            <param name="summary" type="select" label="Summary method">
-                <option value="mean" selected="True">mean=mean value</option>
-                <option value="min">min=minimum value</option>
-                <option value="max">max=maximum value</option>
-                <option value="coverage">coverage=number of covered bases</option>
-                <option value="std">std=standard deviation</option>
+    <xml name="border_color_bed_macro">
+        <conditional name="border_color_bed">
+            <param name="border_color_bed_select" type="select" label="Define border color:">
+                <option value="manually" selected="True">manually</option>
+                <option value="bed_rgb">From the 9th field</option>
+                <option value="none">No border</option>
             </param>
-            <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
-            <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
-                   label="NAN's to zeros" />
-        </section>
+            <when value="manually">
+                <param name="color" type="color" value="#000000" label="Color of the border"/>
+            </when>
+            <when value="bed_rgb" />
+            <when value="none" />
+        </conditional>
     </xml>
     <xml name="bed_advanced_macro">
-        <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
-            <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
-                    label="Global max rows" />
-            <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
-            <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
-            <param name="line_width" type="float" value="0.5" label="width of lines" />
-            <section name ="flybase" title="When using flybase style" expanded="False">
-                <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions in flybase style"/>
-                <param name="color_utr" type="color" value="grey" label="Color of UTR regions"/>
-            </section>
-            <section name ="ucsc" title="When using UCSC style" expanded="False">
-                <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
-            </section>
-            <section name ="gtf" title="When using gtf as input" expanded="False">
-                <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
-                    help="Usually transcript_name or gene_name"/>
-                <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false"
-                    label="Merge all transcripts of each gene in a single entry" />
-            </section>
+        <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                label="Global max rows" />
+        <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
+        <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
+        <param name="line_width" type="float" value="0.5" label="width of lines" />
+        <section name ="gtf" title="When using gtf as input" expanded="False">
+            <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
+                help="Usually transcript_name or gene_name"/>
+            <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                label="Merge all transcripts of each gene in a single entry" />
         </section>
     </xml>
+    <xml name="utr_macro">
+        <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/>
+        <conditional name="color_utr">
+            <param name="color_utr_select" type="select" label="Define UTR color:">
+                <option value="manually" selected="True">manually</option>
+                <option value="bed_rgb">From the 9th field</option>
+                <option value="like">Like the coding</option>
+            </param>
+            <when value="manually">
+                <param name="color" type="color" value="grey" label="Color of UTR regions"/>
+            </when>
+            <when value="bed_rgb" />
+            <when value="like" />
+        </conditional>
+    </xml>
     <xml name="lines_macro">
         <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
         <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/>
@@ -463,157 +166,154 @@
             <option value="dashdot">Dashdot</option>
         </param>
     </xml>
-    <xml name="links_color_macro">
-        <conditional name="color_link">
-            <param name="color_link_select" type="select" label="Use color:">
-                <option value="manually" selected="True">manually</option>
-                <option value="colormap">From the 7th field (score)</option>
-            </param>
-            <when value="manually">
-                <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
-            </when>
-            <when value="colormap">
-              <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
-                <option value="RdYlBu">RdYlBu</option>
-                <option value="Accent">Accent</option>
-                <option value="Spectral">Spectral</option>
-                <option value="Set1">Set1</option>
-                <option value="Set2">Set2</option>
-                <option value="Set3">Set3</option>
-                <option value="Dark2">Dark2</option>
-                <option value="Reds">Reds</option>
-                <option value="Oranges">Oranges</option>
-                <option value="Greens">Greens</option>
-                <option value="Blues">Blues</option>
-                <option value="Greys">Greys</option>
-                <option value="Purples">Purples</option>
-                <option value="Paired">Paired</option>
-                <option value="Pastel1">Pastel1</option>
-                <option value="Pastel2">Pastel2</option>
-                <option value="spring">spring</option>
-                <option value="summer">summer</option>
-                <option value="autumn">autumn</option>
-                <option value="winter">winter</option>
-                <option value="hot">hot</option>
-                <option value="coolwarm">coolwarm</option>
-                <option value="cool">cool</option>
-                <option value="seismic">seismic</option>
-                <option value="terrain">terrain</option>
-                <option value="ocean">ocean</option>
-                <option value="rainbow">rainbow</option>
-                <option value="bone">bone</option>
-                <option value="flag">flag</option>
-                <option value="prism">prism</option>
-                <option value="cubehelix">cubehelix</option>
-                <option value="binary">binary</option>
-                <option value="pink">pink</option>
-                <option value="gray">gray</option>
-                <option value="copper">copper</option>
-                <option value="BrBG">BrBG</option>
-                <option value="BuGn">BuGn</option>
-                <option value="BuPu">BuPu</option>
-                <option value="GnBu">GnBu</option>
-                <option value="OrRd">OrRd</option>
-                <option value="PiYG">PiYG</option>
-                <option value="PRGn">PRGn</option>
-                <option value="PuOr">PuOr</option>
-                <option value="PuRd">PuRd</option>
-                <option value="PuBu">PuBu</option>
-                <option value="RdBu">RdBu</option>
-                <option value="RdGy">RdGy</option>
-                <option value="RdPu">RdPu</option>
-                <option value="YlGn">YlGn</option>
-                <option value="PuBuGn">PuBuGn</option>
-                <option value="RdYlGn">RdYlGn</option>
-                <option value="YlGnBu">YlGnBu</option>
-                <option value="YlOrBr">YlOrBr</option>
-                <option value="YlOrRd">YlOrRd</option>
-                <option value="gist_gray">gist_gray</option>
-                <option value="gist_stern">gist_stern</option>
-                <option value="gist_earth">gist_earth</option>
-                <option value="gist_yarg">gist_yarg</option>
-                <option value="gist_ncar">gist_ncar</option>
-                <option value="gist_rainbow">gist_rainbow</option>
-                <option value="gist_heat">gist_heat</option>
-                <option value="gnuplot">gnuplot</option>
-                <option value="gnuplot2">gnuplot2</option>
-                <option value="CMRmap">CMRmap</option>
-                <option value="bwr">bwr</option>
-                <option value="hsv">hsv</option>
-                <option value="brg">brg</option>
-                <option value="jet">jet</option>
-                <option value="afmhot">afmhot</option>
-                <option value="Accent_r">Accent reversed</option>
-                <option value="Spectral_r">Spectral reversed</option>
-                <option value="Set1_r">Set1 reversed</option>
-                <option value="Set2_r">Set2 reversed</option>
-                <option value="Set3_r">Set3 reversed</option>
-                <option value="Dark2_r">Dark2 reversed</option>
-                <option value="Reds_r">Reds reversed</option>
-                <option value="Oranges_r">Oranges reversed</option>
-                <option value="Greens_r">Greens reversed</option>
-                <option value="Blues_r">Blues reversed</option>
-                <option value="Greys_r">Greys reversed</option>
-                <option value="Purples_r">Purples reversed</option>
-                <option value="Paired_r">Paired reversed</option>
-                <option value="Pastel1_r">Pastel1 reversed</option>
-                <option value="Pastel2_r">Pastel2 reversed</option>
-                <option value="spring_r">spring reversed</option>
-                <option value="summer_r">summer reversed</option>
-                <option value="autumn_r">autumn reversed</option>
-                <option value="winter_r">winter reversed</option>
-                <option value="hot_r">hot reversed</option>
-                <option value="coolwarm_r">coolwarm reversed</option>
-                <option value="cool_r">cool reversed</option>
-                <option value="seismic_r">seismic reversed</option>
-                <option value="terrain_r">terrain reversed</option>
-                <option value="ocean_r">ocean reversed</option>
-                <option value="rainbow_r">rainbow reversed</option>
-                <option value="bone_r">bone reversed</option>
-                <option value="flag_r">flag reversed</option>
-                <option value="prism_r">prism reversed</option>
-                <option value="cubehelix_r">cubehelix reversed</option>
-                <option value="binary_r">binary reversed</option>
-                <option value="pink_r">pink reversed</option>
-                <option value="gray_r">gray reversed</option>
-                <option value="copper_r">copper reversed</option>
-                <option value="BrBG_r">BrBG reversed</option>
-                <option value="BuGn_r">BuGn reversed</option>
-                <option value="BuPu_r">BuPu reversed</option>
-                <option value="GnBu_r">GnBu reversed</option>
-                <option value="OrRd_r">OrRd reversed</option>
-                <option value="PiYG_r">PiYG reversed</option>
-                <option value="PRGn_r">PRGn reversed</option>
-                <option value="PuOr_r">PuOr reversed</option>
-                <option value="PuRd_r">PuRd reversed</option>
-                <option value="PuBu_r">PuBu reversed</option>
-                <option value="RdBu_r">RdBu reversed</option>
-                <option value="RdGy_r">RdGy reversed</option>
-                <option value="RdPu_r">RdPu reversed</option>
-                <option value="YlGn_r">YlGn reversed</option>
-                <option value="PuBuGn_r">PuBuGn reversed</option>
-                <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
-                <option value="RdYlGn_r">RdYlGn reversed</option>
-                <option value="YlGnBu_r">YlGnBu reversed</option>
-                <option value="YlOrBr_r">YlOrBr reversed</option>
-                <option value="YlOrRd_r">YlOrRd reversed</option>
-                <option value="gist_gray_r">gist_gray reversed</option>
-                <option value="gist_stern_r">gist_stern reversed</option>
-                <option value="gist_earth_r">gist_earth reversed</option>
-                <option value="gist_yarg_r">gist_yarg reversed</option>
-                <option value="gist_ncar_r">gist_ncar reversed</option>
-                <option value="gist_rainbow_r">gist_rainbow reversed</option>
-                <option value="gist_heat_r">gist_heat reversed</option>
-                <option value="gnuplot_r">gnuplot reversed</option>
-                <option value="gnuplot2_r">gnuplot2 reversed</option>
-                <option value="CMRmap_r">CMRmap reversed</option>
-                <option value="bwr_r">bwr reversed</option>
-                <option value="hsv_r">hsv reversed</option>
-                <option value="brg_r">brg reversed</option>
-                <option value="jet_r">jet reversed</option>
-                <option value="afmhot_r">afmhot reversed</option>
-              </param>
-            </when>
-        </conditional>
+    <xml name="colormap_macro">
+        <option value="RdYlBu">RdYlBu</option>
+        <option value="Accent">Accent</option>
+        <option value="Spectral">Spectral</option>
+        <option value="Set1">Set1</option>
+        <option value="Set2">Set2</option>
+        <option value="Set3">Set3</option>
+        <option value="Dark2">Dark2</option>
+        <option value="Reds">Reds</option>
+        <option value="Oranges">Oranges</option>
+        <option value="Greens">Greens</option>
+        <option value="Blues">Blues</option>
+        <option value="Greys">Greys</option>
+        <option value="Purples">Purples</option>
+        <option value="Paired">Paired</option>
+        <option value="Pastel1">Pastel1</option>
+        <option value="Pastel2">Pastel2</option>
+        <option value="spring">spring</option>
+        <option value="summer">summer</option>
+        <option value="autumn">autumn</option>
+        <option value="winter">winter</option>
+        <option value="hot">hot</option>
+        <option value="coolwarm">coolwarm</option>
+        <option value="cool">cool</option>
+        <option value="seismic">seismic</option>
+        <option value="terrain">terrain</option>
+        <option value="ocean">ocean</option>
+        <option value="rainbow">rainbow</option>
+        <option value="bone">bone</option>
+        <option value="flag">flag</option>
+        <option value="prism">prism</option>
+        <option value="cubehelix">cubehelix</option>
+        <option value="binary">binary</option>
+        <option value="pink">pink</option>
+        <option value="gray">gray</option>
+        <option value="copper">copper</option>
+        <option value="BrBG">BrBG</option>
+        <option value="BuGn">BuGn</option>
+        <option value="BuPu">BuPu</option>
+        <option value="GnBu">GnBu</option>
+        <option value="OrRd">OrRd</option>
+        <option value="PiYG">PiYG</option>
+        <option value="PRGn">PRGn</option>
+        <option value="PuOr">PuOr</option>
+        <option value="PuRd">PuRd</option>
+        <option value="PuBu">PuBu</option>
+        <option value="RdBu">RdBu</option>
+        <option value="RdGy">RdGy</option>
+        <option value="RdPu">RdPu</option>
+        <option value="YlGn">YlGn</option>
+        <option value="PuBuGn">PuBuGn</option>
+        <option value="RdYlGn">RdYlGn</option>
+        <option value="YlGnBu">YlGnBu</option>
+        <option value="YlOrBr">YlOrBr</option>
+        <option value="YlOrRd">YlOrRd</option>
+        <option value="gist_gray">gist_gray</option>
+        <option value="gist_stern">gist_stern</option>
+        <option value="gist_earth">gist_earth</option>
+        <option value="gist_yarg">gist_yarg</option>
+        <option value="gist_ncar">gist_ncar</option>
+        <option value="gist_rainbow">gist_rainbow</option>
+        <option value="gist_heat">gist_heat</option>
+        <option value="gnuplot">gnuplot</option>
+        <option value="gnuplot2">gnuplot2</option>
+        <option value="CMRmap">CMRmap</option>
+        <option value="bwr">bwr</option>
+        <option value="hsv">hsv</option>
+        <option value="brg">brg</option>
+        <option value="jet">jet</option>
+        <option value="afmhot">afmhot</option>
+        <option value="viridis">viridis</option>
+        <option value="plasma">plasma</option>
+        <option value="inferno">inferno</option>
+        <option value="magma">magma</option>
+        <option value="cividis">cividis</option>
+        <option value="Accent_r">Accent reversed</option>
+        <option value="Spectral_r">Spectral reversed</option>
+        <option value="Set1_r">Set1 reversed</option>
+        <option value="Set2_r">Set2 reversed</option>
+        <option value="Set3_r">Set3 reversed</option>
+        <option value="Dark2_r">Dark2 reversed</option>
+        <option value="Reds_r">Reds reversed</option>
+        <option value="Oranges_r">Oranges reversed</option>
+        <option value="Greens_r">Greens reversed</option>
+        <option value="Blues_r">Blues reversed</option>
+        <option value="Greys_r">Greys reversed</option>
+        <option value="Purples_r">Purples reversed</option>
+        <option value="Paired_r">Paired reversed</option>
+        <option value="Pastel1_r">Pastel1 reversed</option>
+        <option value="Pastel2_r">Pastel2 reversed</option>
+        <option value="spring_r">spring reversed</option>
+        <option value="summer_r">summer reversed</option>
+        <option value="autumn_r">autumn reversed</option>
+        <option value="winter_r">winter reversed</option>
+        <option value="hot_r">hot reversed</option>
+        <option value="coolwarm_r">coolwarm reversed</option>
+        <option value="cool_r">cool reversed</option>
+        <option value="seismic_r">seismic reversed</option>
+        <option value="terrain_r">terrain reversed</option>
+        <option value="ocean_r">ocean reversed</option>
+        <option value="rainbow_r">rainbow reversed</option>
+        <option value="bone_r">bone reversed</option>
+        <option value="flag_r">flag reversed</option>
+        <option value="prism_r">prism reversed</option>
+        <option value="cubehelix_r">cubehelix reversed</option>
+        <option value="binary_r">binary reversed</option>
+        <option value="pink_r">pink reversed</option>
+        <option value="gray_r">gray reversed</option>
+        <option value="copper_r">copper reversed</option>
+        <option value="BrBG_r">BrBG reversed</option>
+        <option value="BuGn_r">BuGn reversed</option>
+        <option value="BuPu_r">BuPu reversed</option>
+        <option value="GnBu_r">GnBu reversed</option>
+        <option value="OrRd_r">OrRd reversed</option>
+        <option value="PiYG_r">PiYG reversed</option>
+        <option value="PRGn_r">PRGn reversed</option>
+        <option value="PuOr_r">PuOr reversed</option>
+        <option value="PuRd_r">PuRd reversed</option>
+        <option value="PuBu_r">PuBu reversed</option>
+        <option value="RdBu_r">RdBu reversed</option>
+        <option value="RdGy_r">RdGy reversed</option>
+        <option value="RdPu_r">RdPu reversed</option>
+        <option value="YlGn_r">YlGn reversed</option>
+        <option value="PuBuGn_r">PuBuGn reversed</option>
+        <option value="RdYlBu_r">RdYlBu reversed</option>
+        <option value="RdYlGn_r">RdYlGn reversed</option>
+        <option value="YlGnBu_r">YlGnBu reversed</option>
+        <option value="YlOrBr_r">YlOrBr reversed</option>
+        <option value="YlOrRd_r">YlOrRd reversed</option>
+        <option value="gist_gray_r">gist_gray reversed</option>
+        <option value="gist_stern_r">gist_stern reversed</option>
+        <option value="gist_earth_r">gist_earth reversed</option>
+        <option value="gist_yarg_r">gist_yarg reversed</option>
+        <option value="gist_ncar_r">gist_ncar reversed</option>
+        <option value="gist_rainbow_r">gist_rainbow reversed</option>
+        <option value="gist_heat_r">gist_heat reversed</option>
+        <option value="gnuplot_r">gnuplot reversed</option>
+        <option value="gnuplot2_r">gnuplot2 reversed</option>
+        <option value="CMRmap_r">CMRmap reversed</option>
+        <option value="bwr_r">bwr reversed</option>
+        <option value="hsv_r">hsv reversed</option>
+        <option value="brg_r">brg reversed</option>
+        <option value="jet_r">jet reversed</option>
+        <option value="afmhot_r">afmhot reversed</option>
+        <option value="viridis_r">viridis reversed</option>
+        <option value="plasma_r">plasma reversed</option>
+        <option value="inferno_r">inferno reversed</option>
+        <option value="magma_r">magma reversed</option>
+        <option value="cividis_r">cividis reversed</option>
     </xml>
 </macros>
--- a/pyGenomeTracks.xml	Tue Feb 11 10:20:24 2020 -0500
+++ b/pyGenomeTracks.xml	Fri Apr 17 11:57:44 2020 -0400
@@ -30,24 +30,20 @@
             #if $region and $region is not None:
                 --region '$region'
             #end if
+            #if $global_args.title is not None:
+                --title '$global_args.title'
+            #end if
+            --fontSize $global_args.fontsize
+            --dpi $global_args.dpi
+            --trackLabelFraction $global_args.trackLabelFraction
+            --trackLabelHAlign $global_args.trackLabelHAlign
             --outFileName plot.$image_file_format
         && mv plot.$image_file_format plot
 ]]>
     </command>
     <configfiles>
         <configfile name="tracks_config">
-## First the xaxis if where = top
-#if $x_axis.x_axis_select == "true":
-  #if $x_axis.where == 'top':
-[x-axis]
-    #if $x_axis.fontsize:
-fontsize = $x_axis.fontsize
-    #end if
-where = top
-  #end if
-#end if
-
-## Then each track:
+## Each track:
 #for $counter, $track in enumerate($tracks):
   ## Hi-C Track
   #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
@@ -124,8 +120,10 @@
       #elif $track.track_file_style_conditional.color_bed.color:
 color = $track.track_file_style_conditional.color_bed.color
       #end if
-      #if $track.track_file_style_conditional.border_color:
-border_color = $track.track_file_style_conditional.border_color
+      #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
+border_color = $track.track_file_style_conditional.border_color_bed.color
+      #else
+border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
       #end if
 display = collapsed
       #if $track.track_file_style_conditional.height_chrom:
@@ -148,8 +146,8 @@
       #set ext = $data_bed.extension
 file = ${counter}_${counter_bed}.$ext
       #if $ext == 'gtf':
-prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name
-merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts
+prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name
+merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts
       #end if
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
@@ -161,33 +159,53 @@
       #elif $track.track_file_style_conditional.color_bed.color:
 color = $track.track_file_style_conditional.color_bed.color
       #end if
-      #if $track.track_file_style_conditional.border_color:
-border_color = $track.track_file_style_conditional.border_color
+      #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
+border_color = $track.track_file_style_conditional.border_color_bed.color
+      #else
+border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
       #end if
-      #if $track.track_file_style_conditional.flybase:
-style = flybase
-height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr
-color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr
-      #else
-style = UCSC
-arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval
+style = $track.track_file_style_conditional.bed_style.bed_style_select
+      #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC':
+arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval
+      #else:
+height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr
+        #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
+color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color
+        #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
+color_utr = bed_rgb
+        #else:
+          #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
+color_utr = bed_rgb
+          #else:
+color_utr = $track.track_file_style_conditional.color_bed.color
+          #end if
+        #end if
+        #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '':
+arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length
+        #end if
+        #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase':
+arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included
+        #end if
       #end if
 display = $track.track_file_style_conditional.display
       #if $track.track_file_style_conditional.height_bed:
 height = $track.track_file_style_conditional.height_bed
       #end if
-labels = $track.track_file_style_conditional.labels
+labels = $track.track_file_style_conditional.labels.plot_labels
+      #if $track.track_file_style_conditional.labels.plot_labels == 'true':
+all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
+labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
+      #end if
 file_type = bed
       #if $track.track_file_style_conditional.fontsize:
 fontsize = $track.track_file_style_conditional.fontsize
       #end if
-      #if $track.track_file_style_conditional.bed_advanced.gene_rows:
-gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows
+      #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
+gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows
       #end if
-global_max_row = $track.track_file_style_conditional.bed_advanced.global_max_row
-max_labels = $track.track_file_style_conditional.bed_advanced.max_labels
-line_width = $track.track_file_style_conditional.bed_advanced.line_width
-arrowhead_included = $track.track_file_style_conditional.arrowhead_included
+global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
+max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
+line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width
       #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
       #end if
@@ -223,6 +241,10 @@
 line_width = $track.track_file_style_conditional.line_width
 line_style = $track.track_file_style_conditional.line_style
 links_type = $track.track_file_style_conditional.links_type
+compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level
+    #if $track.track_file_style_conditional.ylim != "":
+ylim = $track.track_file_style_conditional.ylim
+    #end if
     #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
     #end if
@@ -263,6 +285,7 @@
       #if $track.track_file_style_conditional.height_narrow_peak:
 height = $track.track_file_style_conditional.height_narrow_peak
       #end if
+line_width = $track.track_file_style_conditional.line_width
 show_labels = $track.track_file_style_conditional.show_labels
 file_type = narrow_peak
       #if $track.track_file_style_conditional.fontsize:
@@ -404,13 +427,15 @@
       #if $track.track_file_style_conditional.max_value != "":
 max_value = $track.track_file_style_conditional.max_value
       #end if
-      #if $track.track_file_style_conditional.type_lines:
-type = $track.track_file_style_conditional.type_lines
-      #end if
+type = $track.track_file_style_conditional.type.type_selector
 file_type = bedgraph_matrix
-show_data_range = $track.track_file_style_conditional.show_data
-plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines
-pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin
+      #if $track.track_file_style_conditional.type.type_selector == 'lines':
+show_data_range = $track.track_file_style_conditional.type.show_data
+plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines
+pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin
+      #else
+colormap = $track.track_file_style_conditional.type.colormap
+      #end if
       #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
       #end if
@@ -465,28 +490,83 @@
   ## Spacer
   #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
 [spacer]
+    #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+    #end if
     #if $track.track_file_style_conditional.spacer_height != "":
 height = $track.track_file_style_conditional.spacer_height
     #end if
   #end if
+
+  ## Xaxis:
+  #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option":
+[x-axis]
+    #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+    #end if
+    #if $track.track_file_style_conditional.fontsize != "":
+fontsize = $track.track_file_style_conditional.fontsize
+    #end if
+where = $track.track_file_style_conditional.xaxis_where
+    ## If spacer is asked a new section is created:
+    #if $track.track_file_style_conditional.spacer_height != "":
+[spacer]
+height = $track.track_file_style_conditional.spacer_height
+    #end if
+  #end if
+
+  ## Scale bar:
+  #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option":
+[scale_bar]
+    #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+    #end if
+    #if $track.track_file_style_conditional.color != "":
+color = $track.track_file_style_conditional.color
+    #end if
+alpha = $track.track_file_style_conditional.alpha
+line_width = $track.track_file_style_conditional.line_width
+    #if $track.track_file_style_conditional.x_center != "":
+x_center = $track.track_file_style_conditional.x_center
+    #end if
+    #if $track.track_file_style_conditional.size != "":
+size = $track.track_file_style_conditional.size
+    #end if
+where = $track.track_file_style_conditional.sb_where
+    #if $track.track_file_style_conditional.fontsize != "":
+fontsize = $track.track_file_style_conditional.fontsize
+    #end if
+file_type = scalebar
+    ## If spacer is asked a new section is created:
+    #if $track.track_file_style_conditional.spacer_height != "":
+[spacer]
+height = $track.track_file_style_conditional.spacer_height
+    #end if
+  #end if
 #end for
-
-#if $x_axis.x_axis_select == "true":
-  #if $x_axis.where == 'bottom':
-[x-axis]
-    #if $x_axis.fontsize:
-fontsize = $x_axis.fontsize
-    #end if
-where = bottom
-  #end if
-#end if
 </configfile>
     </configfiles>
     <inputs>
-        <expand macro="region" />
-
+        <!--Arguments for pgt-->
+        <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"
+            help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
+        <section name="global_args" title="Configure figure parameters" expanded="False">
+            <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> 
+            <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
+            <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
+                   help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
+            <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
+                   min="0" max="1"/> 
+            <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
+                <option value="left" selected="True">left</option>
+                <option value="right">right</option>
+                <option value="center">center</option>
+            </param>
+        </section>
+        <!--Info to build the config file-->
         <repeat name="tracks" min="1" title="Include tracks in your plot"
-            help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
+            help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
+            The order you add them represent the order they will be plotted from top to bottom.">
             <conditional name="track_file_style_conditional">
                 <param name="track_file_style_selector" type="select" label="Choose style of the track">
                     <option value="hic_matrix_option">TAD visualization</option>
@@ -501,12 +581,17 @@
                     <option value="vlines_track_option">Vlines track</option>
                     <option value="hlines_track_option">Hlines track</option>
                     <option value="spacer_option">Spacer</option>
+                    <option value="xaxis_option">X-axis</option>
+                    <option value="scale_bar_option">Scale bar track</option>
                 </param>
                 <when value="hic_matrix_option">
                     <expand macro="plot_title" />
                     <expand macro="matrix_h5_cooler_multiple_macro" />
 
-                    <expand macro="colormap" />
+                    <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
+                        <option value="RdYlBu_r">RdYlBu reversed</option>
+                        <expand macro="colormap_macro"/>
+                    </param>
                     <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
                     <expand macro="minmax_macro" />
                     <param name="transform" type="select" label="Plot the transformed value">
@@ -530,7 +615,23 @@
                 <when value="chrom_states_option">
                     <expand macro="plot_title" />
                     <expand macro="track_input_bed_macro" />
-                    <expand macro="color_bed_macro" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" type="select" label="Define color:">
+                            <option value="manually" selected="True">manually</option>
+                            <option value="bed_rgb">From the 9th field</option>
+                            <option value="colormap">From the 5th field (score)</option>
+                        </param>
+                        <when value="manually">
+                            <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+                        </when>
+                        <when value="bed_rgb" />
+                        <when value="colormap">
+                            <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
+                                <expand macro="colormap_macro" />
+                            </param>
+                        </when>
+                    </conditional>
+                    <expand macro="border_color_bed_macro" />
                     <param name="line_width" type="float" value="0.5" label="width of lines" />
                     <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
                     <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
@@ -542,22 +643,75 @@
                     <expand macro="plot_title" />
 
                     <expand macro="track_input_bed_gtf_macro" />
-                    <expand macro="color_bed_macro" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" type="select" label="Define color:">
+                            <option value="manually" selected="True">manually</option>
+                            <option value="bed_rgb">From the 9th field</option>
+                            <option value="colormap">From the 5th field (score)</option>
+                        </param>
+                        <when value="manually">
+                            <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+                        </when>
+                        <when value="bed_rgb" />
+                        <when value="colormap">
+                            <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
+                                <expand macro="colormap_macro" />
+                            </param>
+                        </when>
+                    </conditional>
+                    <expand macro="border_color_bed_macro" />
                     <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
-                    <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
-                            label="Plot labels" />
-                    <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/>
+                    <conditional name="labels">
+                        <param name="plot_labels" type="select" label="Plot labels">
+                            <option value="true" selected="True">yes</option>
+                            <option value="false">no</option>
+                        </param>
+                        <when value="true">
+                            <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                                label="Put all labels inside the plotted region"
+                                help="Put labels on the left of the region if the region ends after the plotted region."/>
+                            <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                                label="Allow to put labels in the right margin"
+                                help="Put labels in the margin if the region ends after the plotted region."/>
+                        </when>
+                        <when value="false"/>
+                    </conditional>
                     <param name="display" type="select" label="display to use">
                         <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
                         <option value="interleaved">interleaved (everything on 2 lines)</option>
                         <option value="collapsed">collapsed (everything on 1 line)</option>
                         <option value="triangles">triangles (plot triangles between start and end)</option>
                     </param>
-                    <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
-                            label="Include the arrowhead in the bed interval:"
-                            help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
                     <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
-                    <expand macro="bed_advanced_macro" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" type="select" label="Bed style">
+                            <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option>
+                            <option value="UCSC">UCSC (blocks with arrows in introns)</option>
+                            <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
+                        </param>
+                        <when value="flybase">
+                            <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                                label="Include the arrowhead in the bed interval:"
+                                help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
+                            <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                                <expand macro="utr_macro" />
+                                <expand macro="bed_advanced_macro" />
+                            </section>
+                        </when>
+                        <when value="UCSC">
+                            <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                                <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
+                                <expand macro="bed_advanced_macro" />
+                            </section>
+                        </when>
+                        <when value="tssarrow">
+                            <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                                <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
+                                <expand macro="utr_macro" />
+                                <expand macro="bed_advanced_macro" />
+                            </section>
+                        </when>
+                    </conditional>
                     <expand macro="overlay_macro" />
                     <expand macro="inverted_macro" />
                     <expand macro="spacer_macro" />
@@ -566,13 +720,32 @@
                 <when value="link_track_option">
                     <expand macro="plot_title" />
                     <expand macro="track_input_link_macro" />
-                    <expand macro="links_color_macro" />
+                    <conditional name="color_link">
+                        <param name="color_link_select" type="select" label="Define color:">
+                            <option value="manually" selected="True">manually</option>
+                            <option value="colormap">From the 7th field (score)</option>
+                        </param>
+                        <when value="manually">
+                            <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+                        </when>
+                        <when value="colormap">
+                            <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
+                                <expand macro="colormap_macro" />
+                            </param>
+                        </when>
+                    </conditional>
                     <expand macro="lines_macro" />
                     <param name="links_type" type="select" label="Representation of the link:">
                         <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
                         <option value="triangles">triangles</option>
                         <option value="loops">loops (a rectangle highlighting the intersection)</option>
                     </param>
+                    <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
+                        <option value="0" selected="True">default (proportional to distance)</option>
+                        <option value="1">compacted (the height is proportional to the square root of the distance)</option>
+                        <option value="2">highly compacted (the height is the same for all distances)</option>
+                    </param>
+                    <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
                     <param name="height" type="float" value="1.5" optional="True" label="height"/>
                     <expand macro="minmax_macro" />
                     <expand macro="overlay_macro" />
@@ -603,6 +776,7 @@
                                    optional="True" label="Plot a vertical bar at the summit position." />
                         </when>
                     </conditional>
+                    <param name="line_width" type="float" value="1" label="width of lines" />
                     <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
                             label="Plot labels (name, p-val, q-val)" />
                     <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
@@ -636,8 +810,18 @@
                     <expand macro="minmax_macro" />
 
                     <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
-                    <expand macro="reading_bw_macro" />
-                    <expand macro="type_coverage_macro" />
+                    <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
+                        <param name="summary" type="select" label="Summary method">
+                            <option value="mean" selected="True">mean=mean value</option>
+                            <option value="min">min=minimum value</option>
+                            <option value="max">max=maximum value</option>
+                            <option value="coverage">coverage=number of covered bases</option>
+                            <option value="std">std=standard deviation</option>
+                        </param>
+                        <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
+                        <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                            label="NAN's to zeros" />
+                    </section>
                     <expand macro="type_coverage_macro" />
                     <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
                     <expand macro="inverted_macro" />
@@ -654,15 +838,30 @@
 
                     <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
 
-                    <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
-                            label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
-                            of the matrix."/>
-                    <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end" help="Only used when type is lines">
-                        <option value="center" selected="True">Center</option>
-                        <option value="block">Block (draw a horizontal line between start and end)</option>
-                    </param>
-                    <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" />
-                    <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
+                    <conditional name="type">
+                        <param name="type_selector" type="select" label="type of plotting">
+                            <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option>
+                            <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option>
+                        </param>
+                        <when value="lines">
+                            <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                                   label="Plot an horizontal line at 0 when type is lines" />
+                            <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                                   label="Show visualization of data range" />
+                            <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end">
+                                <option value="center" selected="True">Center</option>
+                                <option value="block">Block (draw a horizontal line between start and end)</option>
+                            </param>
+                        </when>
+                        <when value="matrix">
+                            <param name="colormap" type="select" label="colormap">
+                                <option value="viridis">Viridis</option>
+                                <expand macro="colormap_macro" />
+                            </param>
+                        </when>
+                    </conditional>
+                    
+                    
                     <expand macro="inverted_macro" />
                     <expand macro="spacer_macro" />
 
@@ -683,28 +882,41 @@
                     <expand macro="spacer_macro" />
                 </when>
                 <when value="spacer_option">
+                    <expand macro="plot_title" />
                     <param name="spacer_height" type="float" value="" optional="True"
                         label="Height of the spacer."/>
                 </when>
+                <when value="xaxis_option">
+                    <expand macro="plot_title" />
+                    <param name="fontsize" type="float" optional="True"
+                        label="Fontsize of the x-axis."/>
+                    <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis">
+                        <option value="bottom" selected="True">below</option>
+                        <option value="top">above</option>
+                    </param>
+                    <expand macro="spacer_macro" />
+                </when>
+                <when value="scale_bar_option">
+                    <expand macro="plot_title" />
+                    <param name="color" type="color" label="Color of the scale bar" optional="True" />
+                    <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
+                    <param name="line_width" type="float" value="0.5" label="width of lines"/>
+                    <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
+                           help="If not set it will be in the middle of the plotted area."/>
+                    <param name="size" type="integer" label="size of the scale bar" optional="True"
+                           help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
+                    <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
+                        <option value="left" selected="True">left</option>
+                        <option value="right">right</option>
+                        <option value="bottom">below</option>
+                        <option value="top">above</option>
+                    </param>
+                    <param name="fontsize" type="float" optional="True"
+                        label="Fontsize of the size of the scale bar."/>
+                    <expand macro="spacer_macro" />
+                </when>
             </conditional>
-
         </repeat>
-
-
-        <conditional name="x_axis">
-            <param name="x_axis_select" type="select" label="Configure x-axis">
-                <option value="false" selected="True">No</option>
-                <option value="true">Yes</option>
-            </param>
-            <when value="true">
-                <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
-                <param name="where" type="select" label="Where to place the x-axis">
-                    <option value="top" selected="True">Top</option>
-                    <option value="bottom">Bottom</option>
-                </param>
-            </when>
-            <when value="false" />
-        </conditional>
         <param name="image_file_format" type="select" label="Image output format">
                 <option value="png">png</option>
                 <option value="svg">svg</option>
@@ -719,17 +931,21 @@
         </data>
     </outputs>
     <tests>
+        <!--test 1-->
         <test>
             <param name="region" value="chrX:3000000-3500000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="hic_matrix_option" />
                     <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
                     <param name="title" value="Kc DpnII (Li et al. 2015)" />
-                    <param name="colormap" value="RdYlBu_r" />
+                    <!--<param name="colormap" value="RdYlBu_r" />-->
                     <param name="depth" value="200000" />
                     <param name="transform" value="log1p" />
                     <param name="boundaries_file" value="domains.bed" />
@@ -758,6 +974,10 @@
                     <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
                     <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
                     <param name="title" value="TAD separation score (Ramirez et al.)" />
+                    <conditional name="type">
+                        <param name="type_selector" value="matrix" />
+                        <!--<param name="colormap" value="viridis" />-->
+                    </conditional>
                     <param name="height_bedgraph" value="10" />
                 </conditional>
             </repeat>
@@ -857,9 +1077,11 @@
                     <param name="title" value="max num rows 3" />
                     <param name="height_bed" value="3" />
                     <param name="fontsize" value="8" />
-                    <section name="bed_advanced">
-                        <param name="gene_rows" value="3" />
-                    </section>
+                    <conditional name="bed_style">
+                        <section name="bed_advanced">
+                            <param name="gene_rows" value="3" />
+                        </section>
+                    </conditional>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -875,9 +1097,11 @@
                     <param name="title" value="bed6 global max row" />
                     <param name="height_bed" value="20" />
                     <param name="fontsize" value="10" />
-                    <section name="bed_advanced">
-                        <param name="global_max_row" value="true" />
-                    </section>
+                    <conditional name="bed_style">
+                        <section name="bed_advanced">
+                            <param name="global_max_row" value="true" />
+                        </section>
+                    </conditional>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -889,11 +1113,15 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 2-->
         <test>
             <param name="region" value="chrX:3000000-3500000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="bigwig_track_option" />
@@ -949,11 +1177,15 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 3-->
         <test>
             <param name="region" value="chrX:3000000-3500000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="hic_matrix_option" />
@@ -1092,7 +1324,9 @@
                     <param name="title" value="genes in ucsc" />
                     <param name="height_bed" value="5" />
                     <param name="fontsize" value="10" />
-                    <param name="flybase" value="false"/>
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                    </conditional>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -1102,9 +1336,11 @@
                     <param name="title" value="bed6 global max row color from score" />
                     <param name="height_bed" value="20" />
                     <param name="fontsize" value="10" />
-                    <section name="bed_advanced">
-                        <param name="global_max_row" value="true" />
-                    </section>
+                    <conditional name="bed_style">
+                        <section name="bed_advanced">
+                            <param name="global_max_row" value="true" />
+                        </section>
+                    </conditional>
                     <conditional name="color_bed">
                         <param name="color_bed_select" value="colormap" />
                         <param name="color" value="RdYlBu_r" />
@@ -1115,26 +1351,66 @@
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="gene_track_option" />
                     <param name="track_input_bed" value="domains.bed" ftype="bed" />
-                    <param name="title" value="domains.bed using the 9th field for colors interleaved" />
+                    <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" />
+                    <param name="height_bed" value="2" />
+                    <param name="fontsize" value="10" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" value="bed_rgb" />
+                    </conditional>
+                    <conditional name="border_color_bed">
+                        <param name="border_color_bed_select" value="manually" />
+                        <param name="color" value="red" />
+                    </conditional>
+                    <conditional name="labels">
+                        <param name="plot_labels" value="false" />
+                    </conditional>
+                    <param name="display" value="interleaved" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="domains.bed" ftype="bed" />
+                    <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" />
                     <param name="height_bed" value="2" />
                     <param name="fontsize" value="10" />
                     <conditional name="color_bed">
                         <param name="color_bed_select" value="bed_rgb" />
                     </conditional>
-                    <param name="border_color" value="red" />
-                    <param name="labels" value="false" />
+                    <conditional name="border_color_bed">
+                        <param name="border_color_bed_select" value="bed_rgb" />
+                    </conditional>
+                    <conditional name="labels">
+                        <param name="plot_labels" value="false" />
+                    </conditional>
+                    <param name="display" value="interleaved" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="domains.bed" ftype="bed" />
+                    <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" />
+                    <param name="height_bed" value="2" />
+                    <param name="fontsize" value="10" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" value="bed_rgb" />
+                    </conditional>
+                    <conditional name="border_color_bed">
+                        <param name="border_color_bed_select" value="none" />
+                    </conditional>
+                    <conditional name="labels">
+                        <param name="plot_labels" value="false" />
+                    </conditional>
                     <param name="display" value="interleaved" />
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 4-->
         <test>
             <param name="region" value="X:2700000-3100000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-                <param name="where" value="bottom" />
-            </conditional>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="bigwig_track_option" />
@@ -1161,14 +1437,24 @@
                     <param name="overlay_select" value="share-y"/>
                 </conditional>
             </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="bottom" />
+                </conditional>
+            </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 5-->
         <test>
             <param name="region" value="X:3000000-3300000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="gene_track_option" />
@@ -1176,7 +1462,9 @@
                     <param name="title" value="test" />
                     <param name="height_bed" value="10" />
                     <param name="color" value="#000000" />
-                    <param name="flybase" value="false" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                    </conditional>
                     <param name="spacer_height" value="1"/>
                 </conditional>
             </repeat>
@@ -1187,19 +1475,18 @@
                     <param name="title" value="test" />
                     <param name="height_bed" value="10" />
                     <param name="color" value="#000000" />
-                    <param name="flybase" value="false" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                    </conditional>
                     <param name="spacer_height" value="1"/>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 6-->
         <test>
             <param name="region" value="X:2760000-2802000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-                <param name="where" value="bottom" />
-            </conditional>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="narrow_peak_track_option" />
@@ -1217,6 +1504,21 @@
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="narrow_peak_track_option" />
+                    <param name="title" value="box line_width = 2" />
+                    <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
+                    <param name="color" value="#9bbb59" />
+                    <param name="height_narrow_peak" value="4" />
+                    <param name="line_width" value="2" />
+                    <conditional name="display">
+                        <param name="display_selector" value="box" />
+                        <param name="use_summit" value="true" />
+                    </conditional>
+                    <param name="show_labels" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="narrow_peak_track_option" />
                     <param name="title" value="peak width 3" />
                     <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
                     <param name="color" value="#c0504d" />
@@ -1247,14 +1549,24 @@
                     <param name="show_labels" value="true" />
                 </conditional>
             </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="bottom" />
+                </conditional>
+            </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 7-->
         <test>
             <param name="region" value="chrX:3300000-3500000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="gene_track_option" />
@@ -1269,37 +1581,110 @@
                     <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
                     <param name="title" value="gtf" />
                     <param name="height_bed" value="10" />
-                    <section name="bed_advanced">
-                        <section name ="flybase">
+                    <conditional name="bed_style">
+                        <section name="bed_advanced">
                             <param name="height_utr" value="0.75"/>
-                            <param name="color_utr" value="#ff0000"/>
+                            <conditional name="color_utr">
+                                <param name="color_utr_select" value="manually"/>
+                                <param name="color" value="#ff0000"/>
+                            </conditional>
+                            <section name ="gtf">
+                                <param name="prefered_name" value="gene_name"/>
+                                <param name="merge_transcripts" value="true"/>
+                            </section>
+                        </section>
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
+                    <param name="title" value="genes with scores" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" value="colormap" />
+                        <param name="color" value="cool_r" />
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
+                    <param name="title" value="genes with utr as bed_rgb" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="bed_style">
+                        <section name="bed_advanced">
+                            <conditional name="color_utr">
+                                <param name="color_utr_select" value="bed_rgb"/>
+                            </conditional>
                         </section>
-                        <section name ="gtf">
-                            <param name="prefered_name" value="gene_name"/>
-                            <param name="merge_transcripts" value="true"/>
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
+                    <param name="title" value="genes with coding as bed_rgb - labels_in_margin" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" value="bed_rgb" />
+                    </conditional>
+                    <conditional name="labels">
+                        <param name="plot_labels" value="true" />
+                        <param name="labels_in_margin" value="true" />
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
+                    <param name="title" value="genes bed_rgb like - all_labels_inside" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="color_bed">
+                        <param name="color_bed_select" value="bed_rgb" />
+                    </conditional>
+                    <conditional name="bed_style">
+                        <section name="bed_advanced">
+                            <conditional name="color_utr">
+                                <param name="color_utr_select" value="like"/>
+                            </conditional>
                         </section>
-                    </section>
+                    </conditional>
+                    <conditional name="labels">
+                        <param name="plot_labels" value="true" />
+                        <param name="all_labels_inside" value="true" />
+                    </conditional>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 8-->
         <test>
             <param name="region" value="chrX:3300000-3500000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="gene_track_option" />
                     <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
                     <param name="title" value="dm3_genes.bed" />
                     <param name="height_bed" value="10" />
-                    <param name="flybase" value="false" />
-                    <section name="bed_advanced">
-                        <param name="global_max_row" value="true" />
-                        <param name="max_labels" value="15" />
-                    </section>
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                        <section name="bed_advanced">
+                            <param name="global_max_row" value="true" />
+                            <param name="max_labels" value="15" />
+                        </section>
+                    </conditional>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -1308,30 +1693,33 @@
                     <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
                     <param name="title" value="genes.bed.gz" />
                     <param name="height_bed" value="10" />
-                    <param name="flybase" value="false" />
-                    <section name="bed_advanced">
-                        <param name="line_width" value="2"/>
-                        <section name ="ucsc">
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                        <section name="bed_advanced">
                             <param name="arrow_interval" value="10"/>
+                            <param name="line_width" value="2"/>
                         </section>
-                    </section>
+                    </conditional>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 9-->
         <test>
             <param name="region" value="X:3133000-3138000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="gene_track_option" />
                     <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
                     <param name="title" value="test" />
                     <param name="height_bed" value="10" />
-                    <param name="flybase" value="true" />
                     <param name="spacer_height" value="1"/>
                 </conditional>
             </repeat>
@@ -1345,7 +1733,9 @@
                         <param name="color_bed_select" value="manually" />
                         <param name="color" value="red" />
                     </conditional>
-                    <param name="flybase" value="false" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                    </conditional>
                     <param name="spacer_height" value="1"/>
                 </conditional>
             </repeat>
@@ -1359,9 +1749,10 @@
                         <param name="color_bed_select" value="manually" />
                         <param name="color" value="red" />
                     </conditional>
-                    <param name="flybase" value="true" />
                     <param name="spacer_height" value="1"/>
-                    <param name="arrowhead_included" value="true"/>
+                    <conditional name="bed_style">
+                        <param name="arrowhead_included" value="true"/>
+                    </conditional>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -1373,11 +1764,15 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 10-->
         <test>
             <param name="region" value="X:3340000-3380000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="gene_track_option" />
@@ -1419,17 +1814,21 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 11-->
         <test>
             <param name="region" value="chrX:3250000-3400000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="hic_matrix_option" />
                     <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
                     <param name="title" value="Kc DpnII (Li et al. 2015)" />
-                    <param name="colormap" value="RdYlBu_r" />
+                    <!--<param name="colormap" value="RdYlBu_r" />-->
                     <param name="depth" value="100000" />
                     <param name="transform" value="log1p" />
                     <param name="show_masked_bins" value="true" />
@@ -1448,10 +1847,12 @@
                     <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
                     <param name="title" value="TAD separation score (Ramirez et al.)" />
                     <param name="height_bedgraph" value="10" />
-                    <param name="type_lines" value="lines" />
-                    <param name="pos_score_in_bin" value="block" />
-                    <param name="plot_horizontal_lines" value="true" />
-                    <param name="show_data" value="true" />
+                    <conditional name="type">
+                        <param name="type_selector" value="lines" />
+                        <param name="pos_score_in_bin" value="block" />
+                        <param name="plot_horizontal_lines" value="true" />
+                        <param name="show_data" value="true" />
+                    </conditional>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -1460,19 +1861,25 @@
                     <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
                     <param name="title" value="TAD separation score (Ramirez et al.)" />
                     <param name="height_bedgraph" value="10" />
-                    <param name="type_lines" value="lines" />
-                    <param name="pos_score_in_bin" value="center" />
-                    <param name="plot_horizontal_lines" value="false" />
+                    <conditional name="type">
+                        <param name="type_selector" value="lines" />
+                        <param name="pos_score_in_bin" value="center" />
+                        <param name="plot_horizontal_lines" value="false" />
+                    </conditional>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 12-->
         <test>
             <param name="region" value="chrX:3000000-3300000"/>
-            <conditional name="x_axis">
-                <param name="x_axis_select" value="true" />
-            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="top" />
+                </conditional>
+            </repeat>
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="hic_matrix_option" />
@@ -1514,6 +1921,156 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 13-->
+        <test>
+            <param name="region" value="chrX:3000000-3300000"/>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="link_track_option" />
+                    <param name="track_input_link" value="test.arcs" ftype="bed" />
+                    <param name="title" value="default" />
+                    <conditional name="color_link">
+                        <param name="color_link_select" value="manually" />
+                        <param name="color" value="#000000" />
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="link_track_option" />
+                    <param name="track_input_link" value="test.arcs" ftype="bed" />
+                    <param name="title" value="ylim 20kb" />
+                    <conditional name="color_link">
+                        <param name="color_link_select" value="manually" />
+                        <param name="color" value="#000000" />
+                    </conditional>
+                    <param name="ylim" value="20000" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="link_track_option" />
+                    <param name="track_input_link" value="test.arcs" ftype="bed" />
+                    <param name="title" value="compacted" />
+                    <conditional name="color_link">
+                        <param name="color_link_select" value="manually" />
+                        <param name="color" value="#000000" />
+                    </conditional>
+                    <param name="compact_arcs_level" value="1" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="link_track_option" />
+                    <param name="track_input_link" value="test.arcs" ftype="bed" />
+                    <param name="title" value="highly compacted" />
+                    <conditional name="color_link">
+                        <param name="color_link_select" value="manually" />
+                        <param name="color" value="#000000" />
+                    </conditional>
+                    <param name="compact_arcs_level" value="2" />
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <!--test 14-->
+        <test>
+            <param name="region" value="chrX:3000000-3300000"/>
+            <section name="global_args">
+                <param name="title" value="Scale bar"/> 
+                <param name="trackLabelFraction" value="0.5"/>
+                <param name="trackLabelHAlign" value="center"/>
+            </section>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="1.0" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="default" />
+                    <param name="spacer_height" value="1"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" />
+                    <param name="color" value="red"/>
+                    <param name="alpha" value="0.5"/>
+                    <param name="line_width" value="2"/>
+                    <param name="x_center" value="3200000"/>
+                    <param name="size" value="100002"/>
+                    <param name="sb_where" value="right"/>
+                    <param name="fontsize" value="8"/>
+                    <param name="spacer_height" value="4"/>
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <!--test 15-->
+        <test>
+            <param name="region" value="chrX:3300000-3500000"/>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="bottom" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
+                    <param name="title" value="flybase" />
+                    <param name="height_bed" value="10" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
+                    <param name="title" value="UCSC" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="UCSC"/>
+                        <section name="bed_advanced">
+                            <param name="arrow_interval" value="10"/>
+                        </section>
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
+                    <param name="title" value="tssarrow" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="tssarrow"/>
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
+                    <param name="title" value="tssarrow 5kb" />
+                    <param name="height_bed" value="10" />
+                    <conditional name="bed_style">
+                        <param name="bed_style_select" value="tssarrow"/>
+                        <section name="bed_advanced">
+                            <param name="arrow_length" value="5000"/>
+                        </section>
+                    </conditional>
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
     </tests>
     <help><![CDATA[
 
Binary file test-data/dm3_genes_withrgbandscore.bed.gz has changed
Binary file test-data/master_TADs_BW_plot.png has changed
Binary file test-data/master_TADs_plot.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test13.ini	Fri Apr 17 11:57:44 2020 -0400
@@ -0,0 +1,49 @@
+[links_1]
+file = test.arcs
+title = default
+height = 1.5
+color = #000000
+alpha = 1.0
+line_width = 0.5
+line_style = solid
+links_type = arcs
+compact_arcs_level = 0
+overlay_previous = no
+file_type = links
+[links_2]
+file = test.arcs
+title = ylim 20kb
+height = 1.5
+color = #000000
+alpha = 1.0
+line_width = 0.5
+line_style = solid
+links_type = arcs
+compact_arcs_level = 0
+ylim = 20000.0
+overlay_previous = no
+file_type = links
+[links_3]
+file = test.arcs
+title = compacted
+height = 1.5
+color = #000000
+alpha = 1.0
+line_width = 0.5
+line_style = solid
+links_type = arcs
+compact_arcs_level = 1
+overlay_previous = no
+file_type = links
+[links_4]
+file = test.arcs
+title = highly compacted
+height = 1.5
+color = #000000
+alpha = 1.0
+line_width = 0.5
+line_style = solid
+links_type = arcs
+compact_arcs_level = 2
+overlay_previous = no
+file_type = links
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test14.ini	Fri Apr 17 11:57:44 2020 -0400
@@ -0,0 +1,23 @@
+[spacer]
+height = 1.0
+[scale_bar]
+title = default
+color = #000000
+alpha = 1.0
+line_width = 0.5
+where = left
+file_type = scalebar
+[spacer]
+height = 1.0
+[scale_bar]
+title = scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5
+color = red
+alpha = 0.5
+line_width = 2.0
+x_center = 3200000
+size = 100002
+where = right
+fontsize = 8.0
+file_type = scalebar
+[spacer]
+height = 4.0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test15.ini	Fri Apr 17 11:57:44 2020 -0400
@@ -0,0 +1,67 @@
+[x-axis]
+where = bottom
+[genes_1_0]
+file = dm3_genes.bed.gz
+title = flybase
+color = #000000
+border_color = #000000
+style = flybase
+height_utr = 1.0
+color_utr = grey
+arrowhead_included = false
+display = stacked
+height = 10.0
+labels = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+overlay_previous = no
+[genes_2_0]
+file = dm3_genes.bed.gz
+title = UCSC
+color = #000000
+border_color = #000000
+style = UCSC
+arrow_interval = 10
+display = stacked
+height = 10.0
+labels = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+overlay_previous = no
+[genes_3_0]
+file = dm3_genes.bed.gz
+title = tssarrow
+color = #000000
+border_color = #000000
+style = tssarrow
+height_utr = 1.0
+color_utr = grey
+display = stacked
+height = 10.0
+labels = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+overlay_previous = no
+[genes_4_0]
+file = dm3_genes.bed.gz
+title = tssarrow 5kb
+color = #000000
+border_color = #000000
+style = tssarrow
+height_utr = 1.0
+color_utr = grey
+arrow_length = 5000
+display = stacked
+height = 10.0
+labels = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+overlay_previous = no
\ No newline at end of file
--- a/test-data/test3.ini	Tue Feb 11 10:20:24 2020 -0500
+++ b/test-data/test3.ini	Fri Apr 17 11:57:44 2020 -0400
@@ -149,7 +149,7 @@
 overlay_previous = no
 [genes_12_0]
 file = test-data/domains.bed
-title = domains.bed using the 9th field for colors interleaved
+title = domains.bed using the 9th field for colors interleaved border=red
 color = bed_rgb
 border_color = red
 style = flybase
@@ -164,4 +164,40 @@
 max_labels = 60
 line_width = 0.5
 arrowhead_included = false
+overlay_previous = no
+[genes_13_0]
+file = test-data/domains.bed
+title = domains.bed using the 9th field for colors interleaved border=bed_rgb
+color = bed_rgb
+border_color = bed_rgb
+style = flybase
+height_utr = 1.0
+color_utr = grey
+display = interleaved
+height = 2.0
+labels = false
+file_type = bed
+fontsize = 10
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
+[genes_14_0]
+file = test-data/domains.bed
+title = domains.bed using the 9th field for colors interleaved border=none
+color = bed_rgb
+border_color = none
+style = flybase
+height_utr = 1.0
+color_utr = grey
+display = interleaved
+height = 2.0
+labels = false
+file_type = bed
+fontsize = 10
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
 overlay_previous = no
\ No newline at end of file
--- a/test-data/test6.ini	Tue Feb 11 10:20:24 2020 -0500
+++ b/test-data/test6.ini	Fri Apr 17 11:57:44 2020 -0400
@@ -10,6 +10,17 @@
 overlay_previous = no
 [narrow_peak_1_0]
 file = test-data/test2.narrowPeak
+title = box line_width = 2
+color = #9bbb59
+type = box
+use_summit = true
+height = 4.0
+show_labels = true
+line_width = 2
+file_type = narrow_peak
+overlay_previous = no
+[narrow_peak_2_0]
+file = test-data/test2.narrowPeak
 title = peak width 3
 color = #c0504d
 type = peak
@@ -23,7 +34,7 @@
 overlay_previous = no
 [spacer]
 height = 0.5
-[narrow_peak_2_0]
+[narrow_peak_3_0]
 file = test-data/test2.narrowPeak
 title = peak no data range
 color = #000000
--- a/test-data/test7.ini	Tue Feb 11 10:20:24 2020 -0500
+++ b/test-data/test7.ini	Fri Apr 17 11:57:44 2020 -0400
@@ -35,4 +35,74 @@
 max_labels = 60
 line_width = 0.5
 arrowhead_included = false
+overlay_previous = no
+[genes_2_0]
+file = test-data/dm3_genes_withrgbandscore.bed.gz
+title = genes with scores
+color = cool_r
+border_color = #000000
+style = flybase
+height_utr = 1.0
+color_utr = grey
+display = stacked
+height = 10.0
+labels = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
+[genes_3_0]
+file = test-data/dm3_genes_withrgbandscore.bed.gz
+title = genes with utr as bed_rgb
+color = black
+border_color = #000000
+style = flybase
+height_utr = 1.0
+color_utr = bed_rgb
+display = stacked
+height = 10.0
+labels = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
+[genes_3_0]
+file = test-data/dm3_genes_withrgbandscore.bed.gz
+title = genes with coding as bed_rgb - labels_in_margin
+color = bed_rgb
+border_color = #000000
+style = flybase
+height_utr = 1.0
+color_utr = grey
+display = stacked
+height = 10.0
+labels = true
+labels_in_margin = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
+[genes_4_0]
+file = test-data/dm3_genes_withrgbandscore.bed.gz
+title = genes bed_rgb like - all_labels_inside
+color = bed_rgb
+border_color = #000000
+style = flybase
+height_utr = 1.0
+color_utr = bed_rgb
+display = stacked
+height = 10.0
+labels = true
+all_labels_inside = true
+file_type = bed
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
 overlay_previous = no
\ No newline at end of file
Binary file test-data/test_arrowhead_zoom.png has changed
Binary file test-data/test_gtf_bed4.png has changed
Binary file test-data/test_gtf_flybase_param.png has changed
Binary file test-data/test_link2.png has changed
Binary file test-data/test_narrowPeak.png has changed
Binary file test-data/test_scale_bar.png has changed
Binary file test-data/test_tssarrow.png has changed
Binary file test-data/test_ucsc_param.png has changed
--- a/test-data/testpyGT.sh	Tue Feb 11 10:20:24 2020 -0500
+++ b/test-data/testpyGT.sh	Fri Apr 17 11:57:44 2020 -0400
@@ -11,5 +11,8 @@
 pgt --tracks test-data/test10.ini --region X:3340000-3380000 -o test-data/test_middle_triangle.png
 pgt --tracks test-data/test11.ini --region chrX:3250000-3400000 -o test-data/test_TADs_bdgm.png
 pgt --tracks test-data/test12.ini --region chrX:3000000-3300000 -o test-data/test_link.png
+pgt --tracks test-data/test13.ini --region chrX:3000000-3300000 -o test-data/test_link2.png
+pgt --tracks test-data/test14.ini --region chrX:3000000-3300000 --title "Scale bar" --trackLabelFraction 0.5 --trackLabelHAlign center -o test-data/test_scale_bar.png
+pgt --tracks test-data/test15.ini --region chrX:3300000-3500000 -o test-data/test_tssarrow.png
 
 conda_env_deactivate