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1 <tool id="SyntenyTrackMapper" name="SyntenyTrackMapper" version="1.0.0">
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2 <description>Compares tracks in .bed-format between two species based on the synteny-based mapping</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 </requirements>
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7
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8 <command>
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9 #if $score.exists == "yes" #java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/trackmapping/TrackMapper $bedfile1 $bedfile2 $mappingFile $score.scoreCol $out_file1
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10 #else # java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/trackmapping/TrackMapper $bedfile1 $bedfile2 $mappingFile -1 $out_file1
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11 #end if
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12 </command>
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13
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14 <inputs>
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15 <param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
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16 <param name="bedfile1" format="bed" type="data" label="Track in .bed-format, species1"/>
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17 <param name="bedfile2" format="bed" type="data" label="Track in .bed-format, species2"/>
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18 <conditional name="score">
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19 <param name="exists" type="select" label=".bed files contain scores">
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20 <option value="yes">Yes</option>
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21 <option value="no">No</option>
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22 </param>
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23 <when value="yes">
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24 <param name="scoreCol" type="data_column" data_ref="bedfile1" label="Score column"/>
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25 </when>
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26 </conditional>
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27 </inputs>
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28 <outputs>
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29 <data format="tabular" name="out_file1" label="Similarity track"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="mappingFile" value="hom_sapi-mus_musc-output-mapping"/>
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34 <param name="bedfile1" value="bed1.bed"/>
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35 <param name="bedfile2" value="bed2.bed"/>
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36 <param name="scoreCol" value="4"/>
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37 <output name="out_file1" file="out_file"/>
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38 </test>
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39 </tests>
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40 <help>
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41
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42 This tool utilizes the gene-based mapping generated with SyntenyMapper to calculate a similarity measure of a track's average gene/intergenic region coverage for two species.
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43
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44 ----
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45
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46 **Input**
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47
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48 .. class:: warningmark
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49
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50 Please make sure that your bed file's genome build is equal to the build used to generate the mapper (*TIP:* Use LiftOver to make it match)
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51
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52 .. class:: infomark
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53
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54 Species 1 and 2 are equal to those chosen by you for SyntenyMapper; if you are unsure about the order, please take a look at the first two rows of the file containing mapped genes.
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55
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56 .. class:: warningmark
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57
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58 Correct input format has to be generated with the SyntenyMapper tool.
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59
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60 Mapped genes is SyntenyMapper's first output file containing 12 columns in the following format:
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61
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62 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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63 |#Species1: homo_sapiens |
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64 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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65 |#Species2: mus_musculus |
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66 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
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67 |#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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68 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
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69 |0 |445330001 |ENSG00000068793 |15 |22892005 |23006016 |ENSMUSG00000030447 |7 |55841745 |55930700 |gene |'no' |
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70 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
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71
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72 ----
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73
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74 **Mapping**
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75
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76 The .bed-entries are divided into segments according to mapping elements (usually genes and intergenic regents), normalized using standard score, and absolute difference between tracks is calculated as a similarity measure. The similarity score will be in column 9 of the resulting similarity track file. Every gene that is not covered by elements in at least one organism has the score -1. Mean score difference for all entries that overlap with at least one element is given in the first comment line of the output.
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77
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78 </help>
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79 </tool>
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