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1 <tool id="fetchflank" name="Fetch flanking bases" version="1.0.0">
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2 <description> of microsatellites and output as two fastq files in forward-forward orientation</description>
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3 <command interpreter="python">pair_fetch_DNA_ff.py $microsat_in_read $Leftflanking $Rightflanking $qualitycutoff $lengthofbasetocheckquality </command>
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4
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5 <inputs>
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6 <param name="microsat_in_read" type="data" label="Select data of microsatellites in reads" />
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7 <param name="qualitycutoff" type="integer" value="20" label="Minimum quality score (Phred+33) for microsatellites and flanking regions" />
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8 <param name="lengthofbasetocheckquality" type="integer" value="20" label="Length of flanking regions that require quality screening" />
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9 </inputs>
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10 <outputs>
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11 <data format="fastq" name="Leftflanking" />
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12 <data format="fastq" name="Rightflanking" />
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13 </outputs>
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14 <tests>
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15 <!-- Test data with valid values -->
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16 <test>
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17 <param name="microsat_in_read" value="samplefq.snoope"/>
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18 <param name="qualitycutoff" value="20"/>
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19 <param name="lengthofbasetocheckquality" value="20"/>
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20 <output name="Leftflanking" file="microsatellite_flanking_L.fastq"/>
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21 <output name="Rightflanking" file="microsatellite_flanking_R.fastq"/>
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22 </test>
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23
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24 </tests>
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25 <help>
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26
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27
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28 .. class:: infomark
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29
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30 **What it does**
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31
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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.
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33
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34 - This tool assumes that the quality score is Phred+33, such as Sanger fastq.
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35 - Reads that have either left or right flanking regions shorter than the length of flanking regions that require quality screening will be removed.
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36
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37 **Citation**
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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**
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39
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40 **Input**
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41
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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**
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43
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44 **Output**
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45
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46 The output will be the two fastq files. The first file contains left flank regions. The second file contains right flanking regions.
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47
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48 **Example**
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49
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50 - Suppose we detected the microsatellites from short reads ::
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51
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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
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53
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54
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55 - We want to get fastq files of flanking regions around microsatellite with quality score at least 20 on Phred +33
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56
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57 - Then the program will report these two fastq files ::
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58
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59 @SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
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60 TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCT
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61 +SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
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62 GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG
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63
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64
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65 @SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
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66 TTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG
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67 +SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
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68 GGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=99(/=5'6=4:CCC*AA
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69
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70
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71
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72 </help>
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73 </tool>
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