Mercurial > repos > s-kaufmann > synteny_mapper
diff visualization.xml @ 2:67eb55a9debe draft
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| author | s-kaufmann |
|---|---|
| date | Mon, 10 Feb 2014 09:06:15 -0500 |
| parents | |
| children | d8da7251bacf |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/visualization.xml Mon Feb 10 09:06:15 2014 -0500 @@ -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="hom_sapi-mus_musc-output-mapping"/> + <param name="syntenyFile" value="hom_sapi-mus_musc-output-synteny"/> + <param name="syntenyRegion" value="44542"/> + <output name="out_file3" file="visualization_test.png"/> + </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>