<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>
    <requirement type="package" version="3.0.2">R_3_0_2</requirement>
    <requirement type="set_environment">R_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 $linear \$R_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>
	<param name="linear" type="select" label="Linear">
			<option value="false">Circular representation</option>
			<option value="true">Linear representation</option>
	</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>