--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualization.xml	Tue May 06 04:23:25 2014 -0400
@@ -0,0 +1,94 @@
+<tool id="SyntenyMapperVisualization1" name="SyntenyMapperVisualization" version="1.0.0">
+  <description>Visualizes micro-rearrangements for one synteny region</description>
+
+<requirements>
+    <requirement type="set_environment">JAR_PATH</requirement>
+    <requirement type="package" version="0.64">circos</requirement>
+    <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
+</requirements>
+
+  <command>
+	java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path
+  </command>
+
+<inputs>
+	<param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
+	<param name="syntenyFile" format="tabular" type="data" size="9" label="Refined synteny regions (SyntenyMapper output2)"/>
+	<param name="syntenyRegion" multiple="False" type="select" label="Choose a synteny region">
+		<options from_dataset="syntenyFile">
+			<column name="name" index="0"/>
+			<column name="value" index="0"/>
+			<!--<filter type="static_value" name="regular" value="regular" column="9"/>
+			<validator type="expression">str(value).find("000") != -1</validator>-->
+			<filter type="sort_by" column="0" ref="syntenyFile"/>
+		</options>
+	</param>
+</inputs>
+  <outputs>
+    <data format="html" name="out_file1" label="Visualization of Mapping"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="mappingFile" value="Gene_mapping1.out"/>
+      <param name="syntenyFile" value="Refined_Synteny_regions2.out"/>
+      <param name="syntenyRegion" value="44454"/>
+      <output name="out_file3" file="visualization_test.html"/>
+    </test>
+  </tests>
+  <help>
+
+This tool visualizes the mapping of genes and out-of-order blocks of genes ("jumped genes") between two organisms for a given synteny region using Circos, effectively illustrating micro-rearrangements.
+
+.. class:: infomark
+
+Gene boxes are clickable and redirect to ENSEMBL.
+
+----
+
+**Input**
+
+.. class:: warningmark
+
+Correct input format has to be generated with the SyntenyMapper tool.
+
+Mapped genes is SyntenyMapper's first output file containing 12 columns in the following format:
+
++---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|#Species1: homo_sapiens                                                                                                                                              |
++---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|#Species2: mus_musculus                                                                                                                                              |
++----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
+|#ID |SyntenyID |ENSEMBL_ID_species1 |Chrom_species1 |Start_species1 |End_species1 |ENSEMBL_ID_species2 |Chrom_species2 |Start_species2 |End_species2 |Type |splitted |
++----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
+|0   |445330001 |ENSG00000068793     |15             |22892005       |23006016     |ENSMUSG00000030447  |7              |55841745       |55930700     |gene |'no'     |
++----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
+
+
+
+Synteny regions need to be updated by SyntenyMapper (second output) and contain information on micro-rearrangements and original synteny blocks in the following format:
+
++------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|#Species1: homo_sapiens                                                                                                                                           |
++------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|#Species2: mus_musculus                                                                                                                                           |
++-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
+|#SyntenyID   |Chrom_species1 |Start_species1 |End_species1 |Direction_species1 |Chrom_species2 |Start_species2 |End_species2 |Direction_species2 |Status          |
++-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
+|"4445500027" |10             |13141449       |13180291     |0                  |2              |5020642        |5064051      |1                  |jumped_internal |
++-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
+|"4460700010" |2              |26987152       |27004099     |0                  |5              |30647933       |30659731     |1                  |jumped_internal |
++-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
+
+----
+
+**Note**
+
+Long synteny region IDs correspond to translocated or inversed regions and will be visualized within the context of their origin synteny region (first 5 digits).
+
+----
+
+**Legend**
+
+.. image::  $PATH_TO_IMAGES/legend.png
+</help>
+</tool>