Mercurial > repos > s-kaufmann > synteny_mapper
comparison track-mapper.xml @ 6:8a4190457eb7 draft
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author | s-kaufmann |
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date | Tue, 06 May 2014 04:23:25 -0400 |
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5:eb0aecd0480c | 6:8a4190457eb7 |
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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="Gene_mapping1.out"/> | |
34 <param name="bedfile1" value="encode-broad-histone-h3k4me1.hg19.bed"/> | |
35 <param name="bedfile2" value="encode-caltech-h3k4me1.mm10.bed"/> | |
36 <param name="scoreCol" value="4"/> | |
37 <output name="out_file1" file="Similarity_track.out"/> | |
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> |