diff pyGenomeTracks.xml @ 8:4ac4e7083b7e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
author iuc
date Tue, 21 Jul 2020 03:32:48 -0400
parents 326a3db8d9d1
children 2824d77cd8f8
line wrap: on
line diff
--- a/pyGenomeTracks.xml	Fri Apr 17 11:57:44 2020 -0400
+++ b/pyGenomeTracks.xml	Tue Jul 21 03:32:48 2020 -0400
@@ -7,7 +7,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code">
 <![CDATA[
-        ## First symlink data of hic or bed/gtf to have the good extension
+        ## First symlink data of hic to have the good extension
         #for $counter, $track in enumerate($tracks):
             #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
                 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
@@ -15,12 +15,6 @@
                     ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
                 #end for
             #end if
-            #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
-                #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
-                    #set ext = $data_bed.extension
-                    ln -s $data_bed ${counter}_${counter_bed}.$ext &&
-                #end for
-            #end if
         #end for
 
 
@@ -38,6 +32,7 @@
             --trackLabelFraction $global_args.trackLabelFraction
             --trackLabelHAlign $global_args.trackLabelHAlign
             --outFileName plot.$image_file_format
+            $global_args.decreasingXAxis
         && mv plot.$image_file_format plot
 ]]>
     </command>
@@ -144,7 +139,7 @@
     #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
 [genes_${counter}_${counter_bed}]
       #set ext = $data_bed.extension
-file = ${counter}_${counter_bed}.$ext
+file = $data_bed
       #if $ext == 'gtf':
 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
@@ -196,7 +191,7 @@
 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
+file_type = $ext
       #if $track.track_file_style_conditional.fontsize:
 fontsize = $track.track_file_style_conditional.fontsize
       #end if
@@ -245,6 +240,7 @@
     #if $track.track_file_style_conditional.ylim != "":
 ylim = $track.track_file_style_conditional.ylim
     #end if
+use_middle = $track.track_file_style_conditional.use_middle
     #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
     #end if
@@ -330,6 +326,7 @@
 max_value = $track.track_file_style_conditional.max_value
       #end if
 show_data_range = $track.track_file_style_conditional.show_data
+grid = $track.track_file_style_conditional.grid
 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
 use_middle = $track.track_file_style_conditional.use_middle
       #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
@@ -345,6 +342,25 @@
         #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
 type = points:$track.track_file_style_conditional.type_conditional.width_point
         #end if
+        #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
+transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
+y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
+          #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
+log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
+          #end if
+        #end if
+      #end if
+      #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no':
+summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method
+        #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins:
+number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins
+        #end if
+      #end if
+      #if $track.track_file_style_conditional.op.operation != 'file':
+operation = $track.track_file_style_conditional.op.operation
+        #if 'second_file' in str($track.track_file_style_conditional.op.operation):
+second_file = $track.track_file_style_conditional.op.second_file
+        #end if
       #end if
       #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
@@ -382,7 +398,7 @@
 max_value = $track.track_file_style_conditional.max_value
       #end if
 height = $track.track_file_style_conditional.height_bigwig
-summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary
+summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method
 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
       #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
@@ -394,7 +410,21 @@
       #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
 type = points:$track.track_file_style_conditional.type_conditional.width_point
       #end if
+      #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
+transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
+y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
+        #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
+log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
+        #end if
+      #end if
+      #if $track.track_file_style_conditional.op.operation != 'file':
+operation = $track.track_file_style_conditional.op.operation
+        #if 'second_file' in $track.track_file_style_conditional.op.operation:
+second_file = $track.track_file_style_conditional.op.second_file
+        #end if
+      #end if
 show_data_range = $track.track_file_style_conditional.show_data
+grid = $track.track_file_style_conditional.grid
 file_type = bigwig
       #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
@@ -451,6 +481,7 @@
   #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
 [vlines_$counter]
 file = $track.track_file_style_conditional.track_input_bed_single
+line_width = $track.track_file_style_conditional.line_width
 type = vlines
   #end if
 
@@ -562,6 +593,8 @@
                 <option value="right">right</option>
                 <option value="center">center</option>
             </param>
+            <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false"
+                label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/>
         </section>
         <!--Info to build the config file-->
         <repeat name="tracks" min="1" title="Include tracks in your plot"
@@ -746,6 +779,10 @@
                         <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="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
+                        <option value="false" selected="True">Extremities (start of first and end of second)</option>
+                        <option value="true">Center (mean of start and end for each)</option>
+                    </param>
                     <param name="height" type="float" value="1.5" optional="True" label="height"/>
                     <expand macro="minmax_macro" />
                     <expand macro="overlay_macro" />
@@ -792,11 +829,29 @@
                     <expand macro="minmax_macro" />
                     <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
                     <expand macro="type_coverage_macro" />
+                    <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False">
+                        <param name="summary_method" type="select" label="Summary method">
+                            <option value="no" selected="True">no=no summary method (keep all values)</option>
+                            <option value="mean">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" />
+                    </section>
+                    <expand macro="logScale_coverage_macro" />
+                    <section name ="op" title="Compute an operation on the file" expanded="False">
+                        <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
+                            help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
+                        <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/>
+                    </section>
                     <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
                         label="NAN's to zeros" />
                     <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false"
                         label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." />
                     <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
+                    <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
                     <expand macro="inverted_macro" />
                     <expand macro="overlay_macro" />
                     <expand macro="spacer_macro" />
@@ -811,7 +866,7 @@
 
                     <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
                     <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
-                        <param name="summary" type="select" label="Summary method">
+                        <param name="summary_method" 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>
@@ -823,7 +878,14 @@
                             label="NAN's to zeros" />
                     </section>
                     <expand macro="type_coverage_macro" />
+                    <expand macro="logScale_coverage_macro" />
+                    <section name ="op" title="Compute an operation on the file" expanded="False">
+                        <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
+                            help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
+                        <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/>
+                    </section>
                     <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
+                    <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
                     <expand macro="inverted_macro" />
                     <expand macro="overlay_macro" />
                     <expand macro="spacer_macro" />
@@ -868,6 +930,7 @@
                 </when>
                 <when value="vlines_track_option">
                     <expand macro="track_input_bed_single_macro" />
+                    <param name="line_width" type="float" value="0.5" label="width of lines"/>
                 </when>
                 <when value="hlines_track_option">
                     <expand macro="plot_title" />
@@ -1280,7 +1343,7 @@
                         <param name="width_point" value="5" />
                     </conditional>
                     <section name="reading_bw_conditional">
-                        <param name="summary" value="max"/>
+                        <param name="summary_method" value="max"/>
                         <param name="number_of_bins" value="100"/>
                     </section>
                 </conditional>
@@ -1295,7 +1358,7 @@
                         <param name="type_selector" value="line_option" />
                     </conditional>
                     <section name="reading_bw_conditional">
-                        <param name="summary" value="min"/>
+                        <param name="summary_method" value="min"/>
                     </section>
                     <param name="overlay_select" value="share-y" />
                 </conditional>
@@ -1310,7 +1373,7 @@
                         <param name="type_selector" value="line_option" />
                     </conditional>
                     <section name="reading_bw_conditional">
-                        <param name="summary" value="min"/>
+                        <param name="summary_method" value="min"/>
                         <param name="number_of_bins" value="30000"/>
                     </section>
                     <param name="overlay_select" value="share-y" />
@@ -1430,7 +1493,7 @@
                     <param name="title" value="" />
                     <param name="color" value="#ff0000" />
                     <param name="alpha" value="0.5" />
-                    <param name="summary" value="max" />
+                    <param name="summary_method" value="max" />
                     <section name="reading_bw_conditional">
                         <param name="number_of_bins" value="300"/>
                     </section>
@@ -2071,6 +2134,481 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <!--test 16-->
+        <test>
+            <param name="region" value="X:2700000-3100000"/>
+            <section name="global_args">
+                <param name="decreasingXAxis" value="true"/>
+            </section>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bigwig_track_option" />
+                    <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                    <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
+                    <param name="height_bigwig" value="7" />
+                    <param name="color" value="#00b0f0" />
+                    <section name="reading_bw_conditional">
+                        <param name="number_of_bins" value="2000"/>
+                    </section>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bigwig_track_option" />
+                    <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                    <param name="title" value="" />
+                    <param name="color" value="#ff0000" />
+                    <param name="alpha" value="0.5" />
+                    <param name="summary_method" value="max" />
+                    <section name="reading_bw_conditional">
+                        <param name="number_of_bins" value="300"/>
+                    </section>
+                    <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_dec.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <!--test 17-->
+        <test>
+            <param name="region" value="chr2:73,800,000-75,744,000"/>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = blue transform = no" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="blue" />
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = blue transform = log" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="blue" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log"/>
+                    </conditional>
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = red transform = log min_value = 1" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="red" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log"/>
+                    </conditional>
+                    <param name="min_value" value="1" />
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="green" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log"/>
+                        <param name="log_pseudocount" value="2"/>
+                    </conditional>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="green" />
+                    <section name="op">
+                        <param name="operation" value="log(2+file)" />
+                    </section>
+                    <param name="min_value" value="0.7" />
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="black" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log2"/>
+                        <param name="log_pseudocount" value="1"/>
+                    </conditional>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="black" />
+                    <section name="op">
+                        <param name="operation" value="log2(1+file)" />
+                    </section>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="black" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log2"/>
+                        <param name="log_pseudocount" value="1"/>
+                        <param name="y_axis_values" value="original"/>
+                    </conditional>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" 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_log.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <!--test 18-->
+        <test>
+            <param name="region" value="chrX:2700000-3100000"/>
+            <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="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
+                    <param name="title" value="file summary_method = mean number_of_bins=20" />
+                    <param name="height_bedgraph" value="4" />
+                    <param name="color" value="blue" />
+                    <param name="show_data" value="true" />
+                    <section name="reading_bdg_as_bw" >
+                        <param name="summary_method" value="mean" />
+                        <param name="number_of_bins" value="20" />
+                    </section>
+                    <param name="min_value" value="0" />
+                    <param name="max_value" value="30" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
+                    <param name="title" value="second_file summary_method = mean" />
+                    <param name="height_bedgraph" value="4" />
+                    <param name="color" value="red" />
+                    <param name="show_data" value="true" />
+                    <section name="reading_bdg_as_bw" >
+                        <param name="summary_method" value="mean" />
+                    </section>
+                    <param name="min_value" value="0" />
+                    <param name="max_value" value="30" />
+                    <param name="spacer_height" value="0.5" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
+                    <param name="title" value="operation = log1p(file) (no summary_method)" />
+                    <param name="height_bedgraph" value="4" />
+                    <param name="color" value="blue" />
+                    <param name="show_data" value="true" />
+                    <section name="op">
+                        <param name="operation" value="log1p(file)" />
+                    </section>
+                    <param name="spacer_height" value="0.5" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
+                    <param name="title" value="operation = file - second_file" />
+                    <param name="height_bedgraph" value="8" />
+                    <param name="color" value="blue" />
+                    <param name="show_data" value="true" />
+                    <conditional name="color_negative">
+                        <param name="color_negative_select" value="true" />
+                        <param name="color" value="red" />
+                    </conditional>
+                    <section name="op">
+                        <param name="operation" value="file - second_file" />
+                        <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
+                    </section>
+                    <param name="min_value" value="-30" />
+                    <param name="max_value" value="30" />
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <!--test 19-->
+        <test>
+            <param name="region" value="chr2:73,800,000-75,744,000"/>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = blue transform = no" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="blue" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = blue transform = log" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="blue" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log"/>
+                    </conditional>
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = red transform = log min_value = 1" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="red" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log"/>
+                    </conditional>
+                    <param name="min_value" value="1" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="green" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log"/>
+                        <param name="log_pseudocount" value="2"/>
+                    </conditional>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="green" />
+                    <section name="op">
+                        <param name="operation" value="log(2+file)" />
+                    </section>
+                    <param name="min_value" value="0.7" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="black" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log2"/>
+                        <param name="log_pseudocount" value="1"/>
+                    </conditional>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="black" />
+                    <section name="op">
+                        <param name="operation" value="log2(1+file)" />
+                    </section>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" value="true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
+                    <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
+                    <param name="height_bedgraph" value="5" />
+                    <param name="color" value="black" />
+                    <conditional name="logScale_conditional">
+                        <param name="transform_selector" value="log2"/>
+                        <param name="log_pseudocount" value="1"/>
+                        <param name="y_axis_values" value="original"/>
+                    </conditional>
+                    <param name="min_value" value="0" />
+                    <param name="show_data" value="true" />
+                    <param name="grid" 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_log_grid.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <!--test 20-->
+        <test>
+            <param name="region" value="chrX:3000000-3300000"/>
+            <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="spacer_option" />
+                    <param name="spacer_height" value="0.05" />
+                </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="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
+                    <param name="depth" value="300000" />
+                    <param name="transform" value="log1p" />
+                    <param name="min_value" value="5" />
+                    <param name="show_masked_bins" value="false" />
+                </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_wide.arcs" ftype="bed" />
+                    <conditional name="color_link">
+                        <param name="color" value="red" />
+                    </conditional>
+                    <param name="line_width" value="5" />
+                    <param name="links_type" value="loops" />
+                    <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="link_track_option" />
+                    <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
+                    <conditional name="color_link">
+                        <param name="color" value="RdYlGn" />
+                    </conditional>
+                    <param name="line_width" value="3" />
+                    <param name="invert_orientation" value="true" />
+                    <param name="title" value="links line_width = 3 color RdYlGn" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="1" />
+                </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="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
+                    <param name="depth" value="300000" />
+                    <param name="transform" value="log1p" />
+                    <param name="min_value" value="5" />
+                    <param name="show_masked_bins" value="false" />
+                </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_wide.arcs" ftype="bed" />
+                    <conditional name="color_link">
+                        <param name="color" value="red" />
+                    </conditional>
+                    <param name="line_width" value="5" />
+                    <param name="links_type" value="loops" />
+                    <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="link_track_option" />
+                    <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
+                    <conditional name="color_link">
+                        <param name="color" value="RdYlGn" />
+                    </conditional>
+                    <param name="line_width" value="3" />
+                    <param name="invert_orientation" value="true" />
+                    <param name="use_middle" value="true" />
+                    <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="vlines_track_option" />
+                    <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
+                    <param name="line_width" value="3" />
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
     </tests>
     <help><![CDATA[