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annotate overlapping_reads.xml @ 4:20d28cfdeefe draft

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author artbio
date Fri, 08 Sep 2017 04:44:22 -0400
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1 <tool id="overlapping_reads" name="Get overlapping reads" version="0.9.3">
1
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2 <description />
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3 <requirements>
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4 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
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10 samtools index '$input' &&
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11 python '$__tool_directory__'/overlapping_reads.py
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12 --input '$input'
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13 --minquery '$minquery'
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14 --maxquery '$maxquery'
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15 --mintarget '$mintarget'
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16 --maxtarget '$maxtarget'
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17 --overlap '$overlap'
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18 --output '$output'
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19 ]]></command>
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20 <inputs>
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21 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
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22 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
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23 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
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24 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
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25 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
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26 <param help="'10' = 10 nucleotides overlap" label="Overlap (in nt)" name="overlap" size="3" type="integer" value="10" />
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27 </inputs>
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28 <outputs>
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29 <data format="fasta" label="pairable reads" name="output" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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34 <param name="minquery" value="23" />
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35 <param name="maxquery" value="29" />
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36 <param name="mintarget" value="23" />
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37 <param name="maxtarget" value="29" />
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38 <param name="overlap" value="10" />
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39 <output file="paired.fa" ftype="fasta" name="output" />
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40 </test>
3
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41 <test>
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42 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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43 <param name="minquery" value="20" />
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44 <param name="maxquery" value="22" />
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45 <param name="mintarget" value="23" />
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46 <param name="maxtarget" value="29" />
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47 <param name="overlap" value="10" />
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48 <output file="paired_2.fa" ftype="fasta" name="output" />
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49 </test>
1
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50 </tests>
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51 <help>
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52
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53 **What it does**
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55 Extract reads with overlap signatures of the specified overlap (in nt) and
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56 return a fasta file of these "pairable" reads.
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58 See `Antoniewski (2014)`_ for background and details
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60 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
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62 **Input**
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63
3
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64 *A **sorted** BAM alignment file.*
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66 *Query and target sizes:*
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67
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68 The algorithm search for each *query* reads (of specified size) in the bam alignment if
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69 there are *target* reads (of specified size) that align on the opposite strand with a 10 nt
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70 overlap.
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72 Searching query reads of 20-22 nt that overlap by 10 nt with target
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73 reads of 23-29 nt is different from searching query reads of 23-29 nt that overlap by 10 nt
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74 with target reads of 20-22 nt. i.e, searching for siRNAs that pair with piRNAs is distinct
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75 from searching for siRNAs that pairs with piRNAs, although of course the number of possibly
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76 formed piRNA/siRNA pairs is the same as the number of possibly formed siRNA/piRNA pairs.
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78 *Overlap*
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79 The number of nucleotides by which the pairs of sequences will overlap
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81
1
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83 **Outputs**
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85 a fasta file of pairable reads such as :
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86
3
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87 >FBgn0000004_17.6|5855|F|23|n=1
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88
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89 TTGACGAAAATGATCGAGTGGAT
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90
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91 >FBgn0000004_17.6|5839|R|26|n=1
1
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92
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93 TTTTCGTCAATTGTGCCAAATAGGTA
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94
3
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95 where FBgn0000004_17.6 stands for the chromosome, 5839 stands for the 1-based read position,
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96 R stand for reverse strand (F forward strand), 26 stands for the size of the sequence and
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97 n=1 stands for the number of reads of the sequence in the dataset.
1
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98
3
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99 the second sequence in this example corresponds to 1 read that overlap by 10 nt with
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100 1 read of the first sequence.
1
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101
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102 </help>
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103 <citations>
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104 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
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105 </citations>
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106 </tool>