--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/track-mapper.xml	Mon Feb 10 09:06:15 2014 -0500
@@ -0,0 +1,79 @@
+<tool id="SyntenyTrackMapper" name="SyntenyTrackMapper" version="1.0.0">
+  <description>Compares tracks in .bed-format between two species based on the synteny-based mapping</description>
+
+<requirements>
+    <requirement type="set_environment">JAR_PATH</requirement>
+</requirements>
+
+  <command>
+	#if $score.exists == "yes" #java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/trackmapping/TrackMapper $bedfile1 $bedfile2 $mappingFile $score.scoreCol $out_file1
+	#else #	java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/trackmapping/TrackMapper $bedfile1 $bedfile2 $mappingFile -1 $out_file1
+	#end if
+  </command>
+
+<inputs>
+	<param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
+	<param name="bedfile1" format="bed" type="data" label="Track in .bed-format, species1"/>
+	<param name="bedfile2" format="bed" type="data" label="Track in .bed-format, species2"/>
+	<conditional name="score">
+		<param name="exists" type="select" label=".bed files contain scores">
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
+		</param>
+	<when value="yes">
+		<param name="scoreCol" type="data_column" data_ref="bedfile1" label="Score column"/>
+	</when>
+	</conditional>
+</inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" label="Similarity track"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="mappingFile" value="hom_sapi-mus_musc-output-mapping"/>
+	<param name="bedfile1" value="bed1.bed"/>
+	<param name="bedfile2" value="bed2.bed"/>
+	<param name="scoreCol" value="4"/>
+      <output name="out_file1" file="out_file"/>
+    </test>
+  </tests>
+  <help>
+
+This tool utilizes the gene-based mapping generated with SyntenyMapper to calculate a similarity measure of a track's average gene/intergenic region coverage for two species.
+
+----
+
+**Input**
+
+.. class:: warningmark
+
+Please make sure that your bed file's genome build is equal to the build used to generate the mapper (*TIP:* Use LiftOver to make it match)
+
+.. class:: infomark
+
+Species 1 and 2 are equal to those chosen by you for SyntenyMapper; if you are unsure about the order, please take a look at the first two rows of the file containing mapped genes.
+
+.. 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'     |
++----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
+
+----
+
+**Mapping**
+
+The .bed-entries are divided into segments according to mapping elements (usually genes and intergenic regents), normalized using standard score, and absolute difference between tracks is calculated as a similarity measure. The similarity score will be in column 9 of the resulting similarity track file. Every gene that is not covered by elements in at least one organism has the score -1. Mean score difference for all entries that overlap with at least one element is given in the first comment line of the output.
+
+</help>
+</tool>