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comparison track-mapper.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 <tool id="SyntenyTrackMapper" name="SyntenyTrackMapper" version="1.0.0">
2 <description>Compares tracks in .bed-format between two species based on the synteny-based mapping</description>
3
4 <requirements>
5 <requirement type="set_environment">JAR_PATH</requirement>
6 </requirements>
7
8 <command>
9 #if $score.exists == "yes" #java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/trackmapping/TrackMapper $bedfile1 $bedfile2 $mappingFile $score.scoreCol $out_file1
10 #else # java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/trackmapping/TrackMapper $bedfile1 $bedfile2 $mappingFile -1 $out_file1
11 #end if
12 </command>
13
14 <inputs>
15 <param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
16 <param name="bedfile1" format="bed" type="data" label="Track in .bed-format, species1"/>
17 <param name="bedfile2" format="bed" type="data" label="Track in .bed-format, species2"/>
18 <conditional name="score">
19 <param name="exists" type="select" label=".bed files contain scores">
20 <option value="yes">Yes</option>
21 <option value="no">No</option>
22 </param>
23 <when value="yes">
24 <param name="scoreCol" type="data_column" data_ref="bedfile1" label="Score column"/>
25 </when>
26 </conditional>
27 </inputs>
28 <outputs>
29 <data format="tabular" name="out_file1" label="Similarity track"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="mappingFile" value="hom_sapi-mus_musc-output-mapping"/>
34 <param name="bedfile1" value="bed1.bed"/>
35 <param name="bedfile2" value="bed2.bed"/>
36 <param name="scoreCol" value="4"/>
37 <output name="out_file1" file="out_file"/>
38 </test>
39 </tests>
40 <help>
41
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.
43
44 ----
45
46 **Input**
47
48 .. class:: warningmark
49
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)
51
52 .. class:: infomark
53
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.
55
56 .. class:: warningmark
57
58 Correct input format has to be generated with the SyntenyMapper tool.
59
60 Mapped genes is SyntenyMapper's first output file containing 12 columns in the following format:
61
62 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
63 |#Species1: homo_sapiens |
64 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------+
65 |#Species2: mus_musculus |
66 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
67 |#ID |SyntenyID |ENSEMBL_ID_species1 |Chrom_species1 |Start_species1 |End_species1 |ENSEMBL_ID_species2 |Chrom_species2 |Start_species2 |End_species2 |Type |splitted |
68 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
69 |0 |445330001 |ENSG00000068793 |15 |22892005 |23006016 |ENSMUSG00000030447 |7 |55841745 |55930700 |gene |'no' |
70 +----+----------+--------------------+---------------+---------------+-------------+--------------------+---------------+---------------+-------------+-----+---------+
71
72 ----
73
74 **Mapping**
75
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.
77
78 </help>
79 </tool>