|
2
|
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>
|
|
3
|
33 <param name="mappingFile" value="Gene_mapping1.out"/>
|
|
|
34 <param name="bedfile1" value="encode-broad-histone-h3k4me1.hg19.bed"/>
|
|
|
35 <param name="bedfile2" value="encode-caltech-h3k4me1.mm10.bed"/>
|
|
2
|
36 <param name="scoreCol" value="4"/>
|
|
3
|
37 <output name="out_file1" file="Similarity_track.out"/>
|
|
2
|
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>
|
