|
6
|
1 <tool id="SyntenyMapperVisualization1" name="SyntenyMapperVisualization" version="1.0.0">
|
|
|
2 <description>Visualizes micro-rearrangements for one synteny region</description>
|
|
|
3
|
|
|
4 <requirements>
|
|
|
5 <requirement type="set_environment">JAR_PATH</requirement>
|
|
|
6 <requirement type="package" version="0.64">circos</requirement>
|
|
|
7 <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
|
|
|
8 </requirements>
|
|
|
9
|
|
|
10 <command>
|
|
|
11 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
|
|
|
12 </command>
|
|
|
13
|
|
|
14 <inputs>
|
|
|
15 <param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
|
|
|
16 <param name="syntenyFile" format="tabular" type="data" size="9" label="Refined synteny regions (SyntenyMapper output2)"/>
|
|
|
17 <param name="syntenyRegion" multiple="False" type="select" label="Choose a synteny region">
|
|
|
18 <options from_dataset="syntenyFile">
|
|
|
19 <column name="name" index="0"/>
|
|
|
20 <column name="value" index="0"/>
|
|
|
21 <!--<filter type="static_value" name="regular" value="regular" column="9"/>
|
|
|
22 <validator type="expression">str(value).find("000") != -1</validator>-->
|
|
|
23 <filter type="sort_by" column="0" ref="syntenyFile"/>
|
|
|
24 </options>
|
|
|
25 </param>
|
|
|
26 </inputs>
|
|
|
27 <outputs>
|
|
|
28 <data format="html" name="out_file1" label="Visualization of Mapping"/>
|
|
|
29 </outputs>
|
|
|
30 <tests>
|
|
|
31 <test>
|
|
|
32 <param name="mappingFile" value="Gene_mapping1.out"/>
|
|
|
33 <param name="syntenyFile" value="Refined_Synteny_regions2.out"/>
|
|
|
34 <param name="syntenyRegion" value="44454"/>
|
|
|
35 <output name="out_file3" file="visualization_test.html"/>
|
|
|
36 </test>
|
|
|
37 </tests>
|
|
|
38 <help>
|
|
|
39
|
|
|
40 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.
|
|
|
41
|
|
|
42 .. class:: infomark
|
|
|
43
|
|
|
44 Gene boxes are clickable and redirect to ENSEMBL.
|
|
|
45
|
|
|
46 ----
|
|
|
47
|
|
|
48 **Input**
|
|
|
49
|
|
|
50 .. class:: warningmark
|
|
|
51
|
|
|
52 Correct input format has to be generated with the SyntenyMapper tool.
|
|
|
53
|
|
|
54 Mapped genes is SyntenyMapper's first output file containing 12 columns in the following format:
|
|
|
55
|
|
|
56 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
|
|
57 |#Species1: homo_sapiens |
|
|
|
58 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
|
|
59 |#Species2: mus_musculus |
|
|
|
60 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
|
|
|
61 |#ID |SyntenyID |ENSEMBL_ID_species1 |Chrom_species1 |Start_species1 |End_species1 |ENSEMBL_ID_species2 |Chrom_species2 |Start_species2 |End_species2 |Type |splitted |
|
|
|
62 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
|
|
|
63 |0 |445330001 |ENSG00000068793 |15 |22892005 |23006016 |ENSMUSG00000030447 |7 |55841745 |55930700 |gene |'no' |
|
|
|
64 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
|
|
|
65
|
|
|
66
|
|
|
67
|
|
|
68 Synteny regions need to be updated by SyntenyMapper (second output) and contain information on micro-rearrangements and original synteny blocks in the following format:
|
|
|
69
|
|
|
70 +------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
|
|
71 |#Species1: homo_sapiens |
|
|
|
72 +------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
|
|
73 |#Species2: mus_musculus |
|
|
|
74 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
|
|
|
75 |#SyntenyID |Chrom_species1 |Start_species1 |End_species1 |Direction_species1 |Chrom_species2 |Start_species2 |End_species2 |Direction_species2 |Status |
|
|
|
76 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
|
|
|
77 |"4445500027" |10 |13141449 |13180291 |0 |2 |5020642 |5064051 |1 |jumped_internal |
|
|
|
78 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
|
|
|
79 |"4460700010" |2 |26987152 |27004099 |0 |5 |30647933 |30659731 |1 |jumped_internal |
|
|
|
80 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
|
|
|
81
|
|
|
82 ----
|
|
|
83
|
|
|
84 **Note**
|
|
|
85
|
|
|
86 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).
|
|
|
87
|
|
|
88 ----
|
|
|
89
|
|
|
90 **Legend**
|
|
|
91
|
|
|
92 .. image:: $PATH_TO_IMAGES/legend.png
|
|
|
93 </help>
|
|
|
94 </tool>
|
