Merge pull request #2710 from bernt-matthias/topic/nw-container-fixes

newick display: add imagemagick dependency

tools/newick_utils/newick_display.xml

@@ -1,10 +1,11 @@
-<tool id="newick_display" name="Newick Display" version="1.6">
+<tool id="newick_display" name="Newick Display" version="1.6+galaxy1">
     <description>visualize a phylogenetic tree</description>
     <edam_operations>
         <edam_operation>operation_0567</edam_operation>
     </edam_operations>
     <requirements>
         <requirement type="package" version="1.6">newick_utils</requirement>
+        <requirement type="package" version="7.0.9_6">imagemagick</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 nw_display
@@ -36,15 +37,13 @@ nw_display
     -w  $width
     $radial
 
-    '$fileNewick' > output.svg
-
-#if $outformat == 'png':
-    && convert output.svg output.png
-    && mv output.png '$output'
-#else:
-    && mv output.svg '$output'
-#end if
+    '$fileNewick'
 
+    #if $outformat == 'png':
+        | convert - 'png:$output'
+    #else:
+        > '$output'
+    #end if
     ]]></command>
     <inputs>
         <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
@@ -112,7 +111,7 @@ nw_display
             <param name="outformat" value="png"/>
             <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
         </test>
-         <test><!-- test with txt output format -->
+        <test><!-- test with txt output format -->
             <param name="fileNewick" value="tree.nwk"/>
             <param name="outformat" value="txt"/>
             <output name="output" file="tree.txt" ftype="txt"/>