# HG changeset patch
# User iuc
# Date 1568927934 14400
# Node ID c237ba7722252b4fb2af8fff1bceadeb36fa5a57
# Parent  feab9265552dda8c6f915301ed73d1fd4be1ae34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"

diff -r feab9265552d -r c237ba772225 macros.xml
--- a/macros.xml	Mon Aug 26 06:20:55 2019 -0400
+++ b/macros.xml	Thu Sep 19 17:18:54 2019 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">3.1</token>
+    <token name="@WRAPPER_VERSION@">3.1.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
@@ -192,6 +192,9 @@
     <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'/>
     </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'/>
+    </xml>
     <xml name="track_input_bed_single_macro">
         <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
     </xml>
diff -r feab9265552d -r c237ba772225 pyGenomeTracks.xml
--- a/pyGenomeTracks.xml	Mon Aug 26 06:20:55 2019 -0400
+++ b/pyGenomeTracks.xml	Thu Sep 19 17:18:54 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.2">
+<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>plot genomic data tracks</description>
     <macros>
         <token name="@BINARY@">pyGenomeTracks</token>
@@ -129,9 +129,7 @@
 #if $track.track_file_style_conditional.height_tad:
 height = $track.track_file_style_conditional.height_tad
 #end if
-#if $track.track_file_style_conditional.show_data:
 show data range = $track.track_file_style_conditional.show_data
-#end if
 
 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
 #if $columns > 4:
@@ -239,6 +237,51 @@
 #end for
 #end if
 
+#if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
+#for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
+
+[narrow_peak_${counter}_${counter_narrow_peak}]
+file = $data_narrow_peak
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_narrow_peak.name
+#end if
+color = $track.track_file_style_conditional.color
+type = $track.track_file_style_conditional.display.display_selector
+use summit = $track.track_file_style_conditional.display.use_summit
+#if $track.track_file_style_conditional.display.display_selector == "peak":
+show data range = $track.track_file_style_conditional.display.show_data
+#if $track.track_file_style_conditional.display.width_adjust:
+width adjust = $track.track_file_style_conditional.display.width_adjust
+#end if
+#if $track.track_file_style_conditional.display.min_value:
+min_value = $track.track_file_style_conditional.display.min_value
+#end if
+#if $track.track_file_style_conditional.display.max_value:
+max_value = $track.track_file_style_conditional.display.max_value
+#end if
+#end if
+
+
+#if $track.track_file_style_conditional.height_narrow_peak:
+height = $track.track_file_style_conditional.height_narrow_peak
+#end if
+
+show labels = $track.track_file_style_conditional.show_labels
+
+file_type = narrow_peak
+#if $track.track_file_style_conditional.fontsize:
+fontsize = $track.track_file_style_conditional.fontsize
+#end if
+
+#if $track.track_file_style_conditional.spacer_height != "":
+[spacer]
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
 
 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
@@ -271,9 +314,7 @@
 max_value = auto
 #end if
 
-#if $track.track_file_style_conditional.show_data:
 show data range = $track.track_file_style_conditional.show_data
-#end if
 
 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
 #if $columns > 4:
@@ -339,9 +380,7 @@
 #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.data_range:
-show data range = $track.track_file_style_conditional.data_range
-#end if
+show data range = $track.track_file_style_conditional.show_data
 file_type = bigwig
 #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
@@ -430,6 +469,7 @@
                     <option value="chrom_states_option">Chromatine states</option>
                     <option value="tad_score_track_option">TAD score</option>
                     <option value="gene_track_option">Gene track / Bed track</option>
+                    <option value="narrow_peak_track_option">NarrowPeak track</option>
                     <option value="bigwig_track_option">Bigwig track</option>
                     <option value="bedgraph_track_option">Bedgraph track </option>
                     <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
@@ -467,7 +507,7 @@
                             label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
                             of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
                     <param name="height_tad" type="float" value="0.2" optional="True" label="height"/>
-                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
+                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" />
                     <expand macro="spacer_macro" />
 
                 </when>
@@ -504,6 +544,36 @@
                     <expand macro="spacer_macro" />
 
                 </when>
+                <when value="narrow_peak_track_option">
+                    <expand macro="plot_title" />
+                    <expand macro="track_input_narrow_peak_macro" />
+                    <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+                    <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
+                    <conditional name="display">
+                        <param name="display_selector" type="select" label="display to use">
+                            <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option>
+                            <option value="box">box: Draw a box</option>
+                        </param>
+                        <when value="peak">
+                            <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true"
+                                   optional="True" label="Use summit information to make the curve." />
+                            <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                                   label="Show visualization of data range" />
+                            <param name='width_adjust' type="float" value="1.5" optional="True" 
+                                   label="Factor to change the width of the curve."/>
+                            <expand macro="minmax_macro" />
+                        </when>
+                        <when value="box">
+                            <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true"
+                                   optional="True" label="Plot a vertical bar at the summit position." />
+                        </when>
+                    </conditional>
+                    <param name="show_labels" type="boolean" truevalue="yes" falsevalue="no" checked="true"
+                            label="Plot labels (name, p-val, q-val)" />
+                    <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+                    <expand macro="spacer_macro" />
+
+                </when>
                 <when value="bedgraph_track_option">
                     <expand macro="plot_title" />
                     <expand macro="track_input_bedgraph_macro" />
@@ -511,7 +581,7 @@
                     <expand macro="minmax_macro" />
                     <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
                     <expand macro="type_coverage_macro" />
-                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
+                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" />
                     <expand macro="inverted_macro" />
                     <expand macro="overlay_macro" />
                     <expand macro="spacer_macro" />
@@ -529,7 +599,7 @@
                     <expand macro="reading_bw_macro" />
                     <expand macro="type_coverage_macro" />
                     <expand macro="type_coverage_macro" />
-                    <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" label="Show visualization of data range"/>
+                    <param name="show_data" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range"/>
                     <expand macro="inverted_macro" />
                     <expand macro="overlay_macro" />
                     <expand macro="spacer_macro" />
@@ -969,7 +1039,9 @@
                     <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" />
-                    <param name="number_of_bins" value="2000"/>
+                    <section name="reading_bw_conditional">
+                        <param name="number_of_bins" value="2000"/>
+                    </section>
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -980,7 +1052,9 @@
                     <param name="color" value="#ff0000" />
                     <param name="alpha" value="0.5" />
                     <param name="summary" value="max" />
-                    <param name="number_of_bins" value="300"/>
+                    <section name="reading_bw_conditional">
+                        <param name="number_of_bins" value="300"/>
+                    </section>
                     <param name="overlay_select" value="share-y"/>
                 </conditional>
             </repeat>
@@ -1017,6 +1091,62 @@
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
         </test>
+        <test>
+            <param name="region" value="X:2760000-2802000"/>
+            <conditional name="x_axis">
+                <param name="x_axis_select" value="yes" />
+                <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" />
+                    <param name="title" value="box" />
+                    <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
+                    <param name="color" value="#9bbb59" />
+                    <param name="height_narrow_peak" value="4" />
+                    <conditional name="display">
+                        <param name="display_selector" value="box" />
+                        <param name="use_summit" value="yes" />
+                    </conditional>
+                    <param name="show_labels" value="yes" />
+                </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" />
+                    <param name="height_narrow_peak" value="4" />
+                    <conditional name="display">
+                        <param name="display_selector" value="peak" />
+                        <param name="use_summit" value="yes" />
+                        <param name="show_data" value="yes" />
+                        <param name="width_adjust" value="3" />
+                        <param name="max_value" value="50" />
+                    </conditional>
+                    <param name="show_labels" value="no" />
+                    <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="narrow_peak_track_option" />
+                    <param name="title" value="peak no data range" />
+                    <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
+                    <param name="color" value="#000000" />
+                    <param name="height_narrow_peak" value="4" />
+                    <conditional name="display">
+                        <param name="display_selector" value="peak" />
+                        <param name="use_summit" value="no" />
+                        <param name="show_data" value="no" />
+                    </conditional>
+                    <param name="show_labels" value="yes" />
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r feab9265552d -r c237ba772225 test-data/bigwig_multiple.png
Binary file test-data/bigwig_multiple.png has changed
diff -r feab9265552d -r c237ba772225 test-data/bigwig_multiple_before.png
Binary file test-data/bigwig_multiple_before.png has changed
diff -r feab9265552d -r c237ba772225 test-data/master_TADs_BW_plot.png
Binary file test-data/master_TADs_BW_plot.png has changed
diff -r feab9265552d -r c237ba772225 test-data/master_TADs_plot.png
Binary file test-data/master_TADs_plot.png has changed
diff -r feab9265552d -r c237ba772225 test-data/master_TADs_plot_before.png
Binary file test-data/master_TADs_plot_before.png has changed
diff -r feab9265552d -r c237ba772225 test-data/test2.narrowPeak
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.narrowPeak	Thu Sep 19 17:18:54 2019 -0400
@@ -0,0 +1,3 @@
+X	2763522	2773887	peak_14338	2505	.	37.31666	253.45494	250.59254	150
+X	2783479	2784861	peak_14339	1676	.	27.80457	170.24620	167.65807	1172
+X	2799191	2799443	peak_14341	885	.	17.74370	90.85378	88.53622	125
diff -r feab9265552d -r c237ba772225 test-data/test_alpha.png
Binary file test-data/test_alpha.png has changed
diff -r feab9265552d -r c237ba772225 test-data/test_narrowPeak.png
Binary file test-data/test_narrowPeak.png has changed