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comparison match.xml @ 8:6bd2945ec360

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author xuebing
date Fri, 16 Mar 2012 14:14:57 -0400
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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 ${on_string} (log)"/>
14 <data format="bed" name="output" label="${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
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
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>