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comparison fetchflank.xml @ 0:70f8259b0b30 draft

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author arkarachai-fungtammasan
date Wed, 01 Apr 2015 16:48:58 -0400
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1 <tool id="fetchflank" name="Fetch flanking bases" version="1.0.0">
2 <description> of microsatellites and output as two fastq files in forward-forward orientation</description>
3 <command interpreter="python">pair_fetch_DNA_ff.py $microsat_in_read $Leftflanking $Rightflanking $qualitycutoff $lengthofbasetocheckquality </command>
4
5 <inputs>
6 <param name="microsat_in_read" type="data" label="Select data of microsatellites in reads" />
7 <param name="qualitycutoff" type="integer" value="20" label="Minimum quality score (Phred+33) for microsatellites and flanking regions" />
8 <param name="lengthofbasetocheckquality" type="integer" value="20" label="Length of flanking regions that require quality screening" />
9 </inputs>
10 <outputs>
11 <data format="fastq" name="Leftflanking" />
12 <data format="fastq" name="Rightflanking" />
13 </outputs>
14 <tests>
15 <!-- Test data with valid values -->
16 <test>
17 <param name="microsat_in_read" value="samplefq.snoope"/>
18 <param name="qualitycutoff" value="20"/>
19 <param name="lengthofbasetocheckquality" value="20"/>
20 <output name="Leftflanking" file="microsatellite_flanking_L.fastq"/>
21 <output name="Rightflanking" file="microsatellite_flanking_R.fastq"/>
22 </test>
23
24 </tests>
25 <help>
26
27
28 .. class:: infomark
29
30 **What it does**
31
32 This tool will fetch flanking regions around microsatellites, screen for quality score at microsatellites and adjacent flanking regions, and output two fastq files containing flanking regions in forward-forward direction.
33
34 - This tool assumes that the quality score is Phred+33, such as Sanger fastq.
35 - Reads that have either left or right flanking regions shorter than the length of flanking regions that require quality screening will be removed.
36
37 **Citation**
38 When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
39
40 **Input**
41
42 The input files need to be in the same format as output from **microsatellite detection program**. This format contains **length of repeat**, **length of left flanking region**, **length of right flanking region**, **repeat motif**, **hamming (editing) distance**, **read name**, **read sequence**, **read quality score**
43
44 **Output**
45
46 The output will be the two fastq files. The first file contains left flank regions. The second file contains right flanking regions.
47
48 **Example**
49
50 - Suppose we detected the microsatellites from short reads ::
51
52 6 40 54 G 0 SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1 TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCTggggggTTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG?FFDFGGGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=99(/=5'6=4:CCC*AA
53
54
55 - We want to get fastq files of flanking regions around microsatellite with quality score at least 20 on Phred +33
56
57 - Then the program will report these two fastq files ::
58
59 @SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
60 TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCT
61 +SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
62 GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG
63
64
65 @SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
66 TTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG
67 +SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
68 GGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=99(/=5'6=4:CCC*AA
69
70
71
72 </help>
73 </tool>