diff hicPlotTADs.xml @ 7:94fff1a6a899 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457

--- a/hicPlotTADs.xml	Tue Jan 02 10:20:13 2018 -0500
+++ b/hicPlotTADs.xml	Wed Mar 07 03:46:02 2018 -0500
@@ -48,6 +48,7 @@
 max_value = $track.track_file_style_conditional.max_value
 #end if
 transform = $track.track_file_style_conditional.transform
+width = $track.track_file_style_conditional.width_matrix
 #if $track.track_file_style_conditional.boundaries_file:
 boundaries_file = $track.track_file_style_conditional.boundaries_file
 #end if
@@ -76,6 +77,9 @@
 #if $track.track_file_style_conditional.width_tad:
 width = $track.track_file_style_conditional.width_tad
 #end if
+#if $track.track_file_style_conditional.type_lines:
+type = $track.track_file_style_conditional.type_lines
+#end if
 #if $track.track_file_style_conditional.show_data:
 show data range = $track.track_file_style_conditional.show_data
 #end if
@@ -246,7 +250,7 @@
                     <option value="hic_matrix_option">TAD visualization</option>
                     <option value="chrom_states_option">Chromatine states</option>
                     <option value="tad_score_track_option">TAD score</option>                    
-                    <option value="gene_track_option">Gene track</option>
+                    <option value="gene_track_option">Gene track / Bed 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>
@@ -267,6 +271,8 @@
                         <option value="-log">-log</option>
                         
                     </param>
+                    <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/>
+                    
                     <param name="type" type="select" optional="True" label="Plotting type">
                         <option value="arcplot">arcplot</option>
                         <option value="interaction">interaction</option>
@@ -282,7 +288,9 @@
                     <expand macro="plot_title" />
                     <expand macro="track_input_bedgraph_macro" />
                     <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
-                    
+                    <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 set to lines if a heatmap representing the matrix is not wanted"/>
                     <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
                     <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />                   
                 </when>