<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="Gene_mapping1.out"/>
	<param name="bedfile1" value="encode-broad-histone-h3k4me1.hg19.bed"/>
	<param name="bedfile2" value="encode-caltech-h3k4me1.mm10.bed"/>
	<param name="scoreCol" value="4"/>
      <output name="out_file1" file="Similarity_track.out"/>
    </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>