Mercurial > repos > artbio > small_rna_signatures

annotate overlapping_reads.xml @ 14:5150d641d515 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
author artbio
date Thu, 06 Apr 2023 23:00:54 +0000
parents 124f404b0fe7
children
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1 <tool id="overlapping_reads" name="Get overlapping reads" version="3.4.2">
1
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2 <description />
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3 <requirements>
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4 <requirement type="package" version="0.18.0">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 ln -f -s $input.metadata.bam_index input.bam.bai &&
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11 ln -s $input input.bam &&
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12 python '$__tool_directory__'/overlapping_reads.py
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13 --input input.bam
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14 --minquery '$minquery'
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15 --maxquery '$maxquery'
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16 --mintarget '$mintarget'
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17 --maxtarget '$maxtarget'
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18 --overlap '$overlap'
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19 --output '$output'
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20 ]]></command>
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21 <inputs>
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22 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
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23 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
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24 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
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25 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
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26 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
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27 <param help="'10' = 10 nucleotides overlap" label="Overlap (in nt)" name="overlap" size="3" type="integer" value="10" />
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28 </inputs>
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29 <outputs>
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30 <data format="fasta" label="pairable reads" name="output" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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35 <param name="minquery" value="23" />
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36 <param name="maxquery" value="29" />
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37 <param name="mintarget" value="23" />
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38 <param name="maxtarget" value="29" />
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39 <param name="overlap" value="10" />
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40 <output file="paired.fa" ftype="fasta" name="output" />
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41 </test>
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42 <test>
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43 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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44 <param name="minquery" value="20" />
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45 <param name="maxquery" value="22" />
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46 <param name="mintarget" value="23" />
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47 <param name="maxtarget" value="29" />
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48 <param name="overlap" value="10" />
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49 <output file="paired_2.fa" ftype="fasta" name="output" />
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50 </test>
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51 <test>
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52 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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53 <param name="minquery" value="23" />
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54 <param name="maxquery" value="29" />
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55 <param name="mintarget" value="20" />
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56 <param name="maxtarget" value="22" />
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57 <param name="overlap" value="10" />
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58 <output file="paired_3.fa" ftype="fasta" name="output" />
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59 </test>
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60 <test>
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61 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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62 <param name="minquery" value="20" />
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63 <param name="maxquery" value="22" />
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64 <param name="mintarget" value="20" />
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65 <param name="maxtarget" value="22" />
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66 <param name="overlap" value="10" />
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67 <output file="paired_4.fa" ftype="fasta" name="output" />
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68 </test>
1
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69 </tests>
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70 <help>
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72 **What it does**
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74 Extract reads with overlap signatures of the specified overlap (in nt) and
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75 return a fasta file of these "pairable" reads.
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76
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77 See `Antoniewski (2014)`_ for background and details
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79 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
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81 **Input**
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82
3
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83 *A **sorted** BAM alignment file.*
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84
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85 *Query and target sizes:*
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86
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87 The algorithm search for each *query* reads (of specified size) in the bam alignment if
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88 there are *target* reads (of specified size) that align on the opposite strand with a 10 nt
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89 overlap.
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90
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91 Searching query reads of 20-22 nt that overlap by 10 nt with target
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92 reads of 23-29 nt is equivalent to searching query reads of 23-29 nt that overlap by 10 nt
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93 with target reads of 20-22 nt. i.e, searching for siRNAs that pair with piRNAs is equivalent
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94 to searching for siRNAs that pairs with piRNAs. In contrast, searching query reads of 20-22 nt
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95 that overlap by 10 nt with target reads of 23-29 nt is different from searching query reads of
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96 23-29 nt that overlap by 10 nt with target reads of 23-29 nt, since the number of "heterotypic"
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97 pairs of reads is likely to be different from the number of "homotypic" pairs of reads.
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98
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99 *Overlap*
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100 The number of nucleotides by which the pairs of sequences will overlap
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101
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102
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103
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104 **Outputs**
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105
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106 a fasta file of pairable reads such as :
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107
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108 >FBgn0000004_17.6|coord=5839|strand -|size=26|nreads=1
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109
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110 TTTTCGTCAATTGTGCCAAATAGGTA
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111
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112 >FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1
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113
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114 TTGACGAAAATGATCGAGTGGAT
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115
1
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116
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117 where FBgn0000004_17.6 stands for the chromosome, 5839 stands for the 1-based read position,
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118 'strand -' stands for lower strand of chromosome, 26 stands for the size of the sequence and
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119 nreads=1 stands for the number of reads of the sequence in the dataset.
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120
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121 the second sequence in this example corresponds to 1 read that overlap by 10 nt with
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122 1 read of the first sequence.
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123
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124 The tool also returns in the standard output the numbers of pairs of reads that
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125 can be formed simultaneously in silico. Note that these numbers are distinct from the numbers
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126 of pairs of read alignments (as computed by the small_rna_signature tool) when analysis is
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127 performed with multi-mapping reads.
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128
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129 </help>
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130 <citations>
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131 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
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132 </citations>
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133 </tool>