--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Haplophyle.xml	Tue Aug 14 08:04:23 2018 -0400
@@ -0,0 +1,227 @@
+<tool id="haplophyle" name="Haplophyle" version="1.0.0">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description>Generates haplotype network</description>
+    
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</requirement>
+        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
+    </requirements>
+    
+
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>    
+
+    <!-- [REQUIRED] The command to execute -->
+    <command interpreter="perl">
+	Haplophyle.sh $input $fileout $dotfile $filelog
+        #if str( $color.choice ) == "yes":
+           $color.input2 $color.groups 
+        #end if
+    </command>
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="input" type="data" format="fasta" optional="false" label="Haplotype sequences in Fasta" />
+        <conditional name="color">
+           <param name="choice" type="boolean" truevalue="yes" falsevalue="no" label="Group colorization?"/>
+           <when value="no">
+           </when>
+           <when value="yes">
+ 	      <param name="input2" type="data" format="txt" optional="true" label="Haplotype sequences and individuals carrying the haplotype" help="See example below"/>
+              <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Semicolon separated file (ind;group)"/>
+           </when>
+        </conditional>
+    </inputs>
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout" format="json" label="JSON for Cytoscape" />
+	<data name="dotfile" format="txt" label="Dot file" />
+	<data name="filelog" format="txt" label="Logfile" />
+    </outputs>
+
+    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
+    <tests>
+        <!-- [HELP] Test files have to be in the ~/test-data directory -->
+        <test>
+            <param name="input" value="haplotype.fasta" />
+            <conditional name="color">
+               <param name="choice" value="yes" />
+               <param name="input2" value="haplotype.txt" />
+               <!--param name="groups" value="" /-->
+            </conditional>
+            <output name="fileout" file="output.json" compare="sim_size" delta="0"/>
+            <output name="dotfile" file="dotfile.txt" compare="sim_size" delta="0"/>
+        </test>
+        <test>
+            <param name="input" value="haplotype.fasta" />
+            <conditional name="color">
+               <param name="choice" value="no" />
+            </conditional>
+            <output name="fileout" file="output.json" compare="sim_size" delta="20"  />
+            <output name="dotfile" file="dotfile.txt" compare="sim_size" delta="0" />
+        </test>
+    </tests>
+
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Authors**     Gautier Sarah : Haplophyle_
+
+.. _Haplophyle: http://haplophyle.cirad.fr/Haplophyle/
+
+.. class:: infomark
+
+**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
+
+.. class:: infomark
+
+**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
+
+---------------------------------------------------
+
+================
+Haplophyle
+================
+
+-----------
+Description
+-----------
+
+  | Create haplotype network from haplotype sequences
+
+----------
+Input file
+----------
+
+Haplotype fasta file
+	Haplotype fasta file with haplotype sequences and proportion
+Haplotype sequences and their individuals
+	Haplotype sequences and list of individuals holding the haplotype
+
+Groups
+
+------------
+Output files
+------------
+
+JSON file for Cytoscape
+Dot file
+Log file
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+Haplotype fasta file
+----------------------------
+
+::
+
+	>haplo1|1
+	AGAGGCCCATT
+	>haplo2|1
+	CGAGGTCCATT
+	>haplo3|1
+	CGGAGCCCATT
+	>haplo4|2
+	AGAGGTCTATT
+	>haplo5|1
+	CGAGGTCTATT
+	>haplo6|7
+	AGAGGTCCATT
+	>haplo7|3
+	CAAGATCCATC
+	>haplo8|1
+	CGAGGTTCATT
+	>haplo9|1
+	CGGAGCCCGTT
+	>haplo10|1
+	CGAGGCCCATT
+	>haplo11|1
+	AGAGGTTCATT
+	>haplo12|38
+	CAAGGTCCATT
+	>haplo13|3
+	CAAGGTCCACT
+	>haplo14|1
+	AGGAGCCCATT
+
+
+Haplotype sequences and their individuals
+----------------------------------------------
+
+::
+
+        haplo4:2:RS10_1,RS10_2,
+        GAGTGGGTTGCTTCCTTGCGTAGCCATCCGCCAACGACTGT
+        haplo5:2:RC3_1,RC3_2,
+        AGGTATACTGCCTGCTCGCGTAGTCAGCCGCCGACGGCTGG
+        haplo6:2:RS8_1,RS8_2,
+        GAGTGGGTTGCTTCCTTGCGTAGCCATCCACCAACGACTGT
+        haplo7:2:sativa_1,sativa_2,
+        GAGTGGGCTGCTTCCTCGCGTAGTCAGCCGCCGACAGCTGG
+
+
+
+Output files
+============
+
+output.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"} }]}}
+
+
+dotfile.txt
+----------------------------
+
+::
+
+	graph G {
+	overlap="scale";
+	outputMode="nodesfirst";
+	MV1 [shape="circle", color="red", width=0.1, height=0.1,fixedsize=true];
+	MV2 [shape="circle", color="red", width=0.1, height=0.1,fixedsize=true];
+	haplo2 [shape="circle",style="filled", color="green" , imagescale="both", width=0.8, height=0.8,fixedsize=true];
+	haplo4 [shape="circle",style="filled", color="green" , imagescale="both", width=0.8, height=0.8,fixedsize=true];
+	haplo8 [shape="circle",style="filled", color="green" , imagescale="both", width=0.8, height=0.8,fixedsize=true];
+	haplo7 -- MV2 [len=0.2];
+	haplo1 -- haplo2 [len=0.2];
+	haplo4 -- MV1 [len=0.2];
+	MV2 -- MV3 [len=0.6];
+	haplo5 -- MV3 [len=0.8];
+	haplo8 -- MV3 [len=1,label="length: 24.0",color="red"];
+	}
+
+        
+
+
+    ]]></help>
+
+</tool>