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comparison visualization.xml @ 2:67eb55a9debe draft

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author s-kaufmann
date Mon, 10 Feb 2014 09:06:15 -0500
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1:7601ef706058 2:67eb55a9debe
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="hom_sapi-mus_musc-output-mapping"/>
33 <param name="syntenyFile" value="hom_sapi-mus_musc-output-synteny"/>
34 <param name="syntenyRegion" value="44542"/>
35 <output name="out_file3" file="visualization_test.png"/>
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>