|
2
|
1 <tool id="match" name="match">
|
|
|
2 <description>find short motif occurrences</description>
|
|
|
3 <command> ./match $motif $seq $output $nmismatch $rc $bed > $log</command>
|
|
|
4 <inputs>
|
|
|
5
|
|
|
6 <param name="motif" type="data" format="fasta" label="Search occurances of the following motifs" help="one or multiple sequences, FASTA format"/>
|
|
|
7 <param name="seq" type="data" format="fasta" label="in sequences" help="one or multiple sequences, FASTA format"/>
|
|
|
8 <param name="nmismatch" size="10" type="integer" value="0" label="number of mismatches allowed"/>
|
|
|
9 <param name="rc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="norc" falsevalue="rc" checked="False"/>
|
|
|
10 <param name="bed" label="output BED format" help="Default is tabular file (see example below). Please only check this if your sequence identifier looks like: hg18_chr6_122208322_122209078_+ (true for galaxy tool extracted sequences)" type="boolean" truevalue="bed" falsevalue="nobed" checked="True"/>
|
|
|
11 </inputs>
|
|
|
12 <outputs>
|
|
|
13 <data format="log" name="log" label="${tool.name} on ${on_string} (log)"/>
|
|
|
14 <data format="bed" name="outfile" label="${tool.name} on ${on_string} (bed)"/>
|
|
|
15 </outputs>
|
|
|
16 <help>
|
|
|
17
|
|
|
18 **What it does**
|
|
|
19
|
|
|
20 This tool searches occurrences of a short nucleotide seuqences (allowing mismatches) in a set of longer sequences.
|
|
|
21
|
|
|
22 Example motif file::
|
|
|
23
|
|
|
24 >motif1
|
|
|
25 CAGGTAAGT
|
|
|
26 >motif2
|
|
|
27 GTTTGGGGGCC
|
|
|
28
|
|
|
29 Example sequence file::
|
|
|
30
|
|
|
31 >hg18_chr6_122208322_122209078_+
|
|
|
32 CGTCGTAGCTACTAGCTACGTACGTACGTAGCTAGCATGCATGCTACGTA
|
|
|
33 CGTAGCTAGCTAAAAAAAAAAAAAAACTGCGGCTAGCTAGCTAGCTACGT
|
|
|
34 CGATCGTAGCTAC...
|
|
|
35 >hg18_chr6_1208322_122209023_+
|
|
|
36 CGATGCTAGCTAGCTAGCTACGTAGCTAGCTAGTCGATGCTAGCTAGCTA
|
|
|
37 ATGCTAGCTAGC....
|
|
|
38
|
|
|
39 Output (bed)::
|
|
|
40
|
|
6
|
41 chr11 72790893 72790902 ACTTAACTG 1 - antisense 5ss,G4T:CAGTTAAGT-rc hg18_chr11_72790846_72791902_+ 47
|
|
|
42 chr11 72791880 72791889 CAGGTAAGA 1 + sense 5ss,T9A:CAGGTAAGA hg18_chr11_72790846_72791902_+ 1034
|
|
2
|
43
|
|
|
44
|
|
|
45 Output (tab)::
|
|
|
46
|
|
|
47 Tmod4 802 5ss:CAGGTAAGT-rc ACTTACCTG
|
|
|
48 Atp7b 77 5ss:CAGGTAAGT CAGGTAAGT
|
|
|
49 Fnta 665 5ss:CAGGTAAGT CAGGTAAGT
|
|
|
50
|
|
|
51
|
|
|
52
|
|
|
53 </help>
|
|
|
54 </tool>
|
