# HG changeset patch
# User vmarcon
# Date 1533298284 14400
# Node ID 0e4dc43800b8a78c4fc1ef73ab5e8b9685ce0432
# Parent  6bf83148cae725a037a483b93c5fc12546f2930e
planemo upload commit d28e54b122131899c7ec49abc39f72645da36ecf-dirty

diff -r 6bf83148cae7 -r 0e4dc43800b8 Cytoscape.xml
--- a/Cytoscape.xml	Thu Aug 02 11:18:49 2018 -0400
+++ b/Cytoscape.xml	Fri Aug 03 08:11:24 2018 -0400
@@ -41,7 +41,7 @@
     </tests>    
 
     <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
+    <help><![CDATA[
 
 .. class:: infomark
 
@@ -51,7 +51,7 @@
 
 .. class:: infomark
 
-**Galaxy integration** Alexis Dereeper, IRD.
+**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
 
 .. class:: infomark
 
@@ -82,6 +82,40 @@
 Cytoscape network
 
 Log file
-    </help>
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input file
+==========
+
+input.json
+----------------------------
+
+::
+
+        {"elements": {"nodes": [{ "data": { "id": "MV1", "width": 0.1} },
+        { "data": { "id": "MV2", "width": 0.1} },
+        { "data": { "id": "MV3", "width": 0.1} },
+        { "data": { "id": "haplo6", "width": 0.8 } },
+        { "data": { "id": "haplo7", "width": 0.8 } },
+        { "data": { "id": "haplo8", "width": 0.8 } }],
+        "edges": [
+        { "data": { "id": "haplo4MV1", "weight": 1, "source": "haplo4", "target": "MV1"} },
+        { "data": { "id": "haplo3haplo4", "weight": 1, "source": "haplo3", "target": "haplo4"} },
+        { "data": { "id": "haplo5MV3", "weight": 1, "source": "haplo5", "target": "MV3"} },
+        { "data": { "id": "MV1MV2", "weight": 1, "source": "MV1", "target": "MV2"} },
+        { "data": { "id": "haplo8MV3", "weight": 1, "source": "haplo8", "target": "MV3"} }]}}
+
+input.json
+----------------------------
+
+.. image:: $PATH_TO_IMAGES/network.png
+   :width: 500 px
+
+   ]]></help>
 
 </tool>
diff -r 6bf83148cae7 -r 0e4dc43800b8 static/images/network.png
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diff -r 6bf83148cae7 -r 0e4dc43800b8 static/images/out.insertion_profile.R1.png
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diff -r 6bf83148cae7 -r 0e4dc43800b8 static/images/out.insertion_profile.R2.png
Binary file static/images/out.insertion_profile.R2.png has changed