diff hifive.xml @ 1:cb4f92e6fd4e draft

planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d

--- a/hifive.xml	Fri Jun 05 14:09:00 2015 -0400
+++ b/hifive.xml	Wed Aug 26 16:53:42 2015 -0400
@@ -74,6 +74,13 @@
 	#end if
 	$hic_project $hic_int_output
 #end if
+#if str( $command.command_select ) == "hic-mrheatmap":
+	@HIC_CHROMOSOMES@
+	@HIC_DATATYPE@
+	$command.trans1
+	@MRH_OPTIONS@
+	$hic_project $hic_mrheatmap
+#end if
 #if str( $command.command_select ) == "5c-complete":
 	@5C_NORMALIZE@
 	@5C_SEQUENCE@
@@ -148,6 +155,7 @@
 				<option value="hic-normalize">Normalize HiC project</option>
 				<option value="hic-heatmap">Create HiC heatmap set</option>
 				<option value="hic-interval">Extract HiC interval</option>
+				<option value="hic-mrheatmap">Create HiC multi-resolution heatmap</option>
 				<option value="fragments">Create 5C fragment set</option>
 				<option value="5c-data">Create 5C data set</option>
 				<option value="5c-project">Create 5C project</option>
@@ -232,6 +240,16 @@
 		            <when value="no"/>
 		        </conditional>
 		    </when>
+		   	<when value="hic-mrheatmap">
+		        <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/>
+				<expand macro="hic_chromosomes_xml"/>
+		        <param type="select" name="trans1" label="Calculate and include trans interactions">
+		            <option value="-t">yes</option>
+		            <option value="">no</option>
+		        </param>
+		        <expand macro="mrh_options_xml"/>
+		        <expand macro="hic_datatype_xml"/>
+			</when>
 			<when value="5c-complete">
 				<expand macro="5c_fragment_xml"/>
 				<expand macro="5c_sequence_xml"/>
@@ -344,6 +362,9 @@
         	<filter>(command["command_select"] == "hic-interval")</filter>
             <filter>(command["image"]["generate"] == "yes")</filter>
         </data>
+        <data format="mrh" name="hic_mrheatmap" label="${tool.name} on ${on_string}: HiC MR-heatmap">
+        	<filter>(command["command_select"] == "hic-mrheatmap")</filter>
+        </data>
         <data format="h5" name="fivec_comp_frags" label="${tool.name} on ${on_string}: 5C frags">
         	<filter>(command["command_select"] == "5c-complete")</filter>
         </data>