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1 <tool id="SyntenyMapperVisualization1" name="SyntenyMapperVisualization" version="1.0.0">
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2 <description>Visualizes micro-rearrangements for one synteny region</description>
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3
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4 <requirements>
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5 <requirement type="set_environment">JAR_PATH</requirement>
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6 <requirement type="package" version="0.64">circos</requirement>
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7 <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
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20
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8 <requirement type="package" version="3.0.2">R_3_0_2</requirement>
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10
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9 <requirement type="set_environment">R_PATH</requirement>
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10 </requirements>
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11
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12 <command>
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13 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
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14 </command>
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15
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16 <inputs>
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17 <param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
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18 <param name="syntenyFile" format="tabular" type="data" size="9" label="Refined synteny regions (SyntenyMapper output2)"/>
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19 <param name="syntenyRegion" multiple="False" type="select" label="Choose a synteny region">
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20 <options from_dataset="syntenyFile">
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21 <column name="name" index="0"/>
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22 <column name="value" index="0"/>
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23 <!--<filter type="static_value" name="regular" value="regular" column="9"/>
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24 <validator type="expression">str(value).find("000") != -1</validator>-->
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25 <filter type="sort_by" column="0" ref="syntenyFile"/>
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26 </options>
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27 </param>
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28 <param name="linear" type="select" label="Linear">
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29 <option value="false">Circular representation</option>
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30 <option value="true">Linear representation</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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25
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34 <data format="html" name="out_file1" label="Visualization of Mapping">
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35 <filter>linear=='false'</filter>
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36 </data>
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37 <data format="pdf" name="out_file1" label="Visualization of Mapping">
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38 <filter>linear=='true'</filter>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="mappingFile" value="Gene_mapping1.out"/>
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44 <param name="syntenyFile" value="Refined_Synteny_regions2.out"/>
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45 <param name="syntenyRegion" value="44454"/>
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46 <output name="out_file3" file="visualization_test.html"/>
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47 </test>
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48 </tests>
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49 <help>
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50
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51 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.
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52
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53 .. class:: infomark
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54
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55 Gene boxes are clickable and redirect to ENSEMBL.
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56
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57 ----
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58
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59 **Input**
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60
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61 .. class:: warningmark
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62
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63 Correct input format has to be generated with the SyntenyMapper tool.
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64
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65 Mapped genes is SyntenyMapper's first output file containing 12 columns in the following format:
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66
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67 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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68 |#Species1: homo_sapiens |
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69 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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70 |#Species2: mus_musculus |
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71 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
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72 |#ID |SyntenyID |ENSEMBL_ID_species1 |Chrom_species1 |Start_species1 |End_species1 |ENSEMBL_ID_species2 |Chrom_species2 |Start_species2 |End_species2 |Type |splitted |
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73 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
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74 |0 |445330001 |ENSG00000068793 |15 |22892005 |23006016 |ENSMUSG00000030447 |7 |55841745 |55930700 |gene |'no' |
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75 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
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76
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77
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78
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79 Synteny regions need to be updated by SyntenyMapper (second output) and contain information on micro-rearrangements and original synteny blocks in the following format:
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80
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81 +------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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82 |#Species1: homo_sapiens |
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83 +------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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84 |#Species2: mus_musculus |
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85 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
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86 |#SyntenyID |Chrom_species1 |Start_species1 |End_species1 |Direction_species1 |Chrom_species2 |Start_species2 |End_species2 |Direction_species2 |Status |
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87 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
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88 |"4445500027" |10 |13141449 |13180291 |0 |2 |5020642 |5064051 |1 |jumped_internal |
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89 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
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90 |"4460700010" |2 |26987152 |27004099 |0 |5 |30647933 |30659731 |1 |jumped_internal |
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91 +-------------+---------------+---------------+-------------+-------------------+---------------+---------------+-------------+-------------------+----------------+
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92
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93 ----
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94
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95 **Note**
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96
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97 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).
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98
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99 ----
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100
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101 **Legend**
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102
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103 .. image:: $PATH_TO_IMAGES/legend.png
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104 </help>
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105 </tool>
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