diff hicPlotTADs.xml @ 5:144bf28956a7 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

--- a/hicPlotTADs.xml	Sat Dec 16 16:36:29 2017 -0500
+++ b/hicPlotTADs.xml	Sat Dec 30 09:34:14 2017 -0500
@@ -7,6 +7,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code">
 <![CDATA[
+
         sed '/^$/d' '$tracks_config' &&
         @BINARY@
             --tracks '$tracks_config'
@@ -31,7 +32,7 @@
 #for $counter, $track in enumerate($tracks):
 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":  
 [hic_section_$counter]
-file = $track.track_file_style_conditional.track_input_h5
+file = $track.track_file_style_conditional.matrix_h5_cooler
 file_type = hic_matrix
 title = $track.track_file_style_conditional.title
 #if $track.track_file_style_conditional.depth:
@@ -254,7 +255,7 @@
                 </param>
                 <when value="hic_matrix_option">
                     <expand macro="plot_title" />
-                    <expand macro="track_input_h5_macro" />
+                    <expand macro="matrix_h5_cooler_macro" />
                     
                     <expand macro="colormap" />
                     <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
@@ -413,7 +414,8 @@
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="hic_matrix_option" />
-                    <param name="track_input_h5" value="Li_et_al_2015.h5" ftype="h5" />
+                    <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+
                     <param name="title" value="Kc DpnII (Li et al. 2015)" />
                     <param name="colormap" value="RdYlBu_r" />
                     <param name="depth" value="200000" />