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comparison overlapping_reads.xml @ 1:6f1378738798 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
author artbio
date Tue, 29 Aug 2017 20:02:15 -0400
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1 <tool id="overlapping_reads" name="Get overlapping reads" version="0.9.0">
2 <description />
3 <requirements>
4 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[
10 samtools index '$input' &&
11 python '$__tool_directory__'/overlapping_reads.py
12 --input '$input'
13 --minquery '$minquery'
14 --maxquery '$maxquery'
15 --mintarget '$mintarget'
16 --maxtarget '$maxtarget'
17 --overlap '$overlap'
18 --output '$output'
19 ]]></command>
20 <inputs>
21 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
22 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
23 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
24 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
25 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
26 <param help="'10' = 10 nucleotides overlap" label="Overlap (in nt)" name="overlap" size="3" type="integer" value="10" />
27 </inputs>
28 <outputs>
29 <data format="fasta" label="pairable reads" name="output" />
30 </outputs>
31 <tests>
32 <test>
33 <param ftype="bam" name="input" value="sr_bowtie.bam" />
34 <param name="minquery" value="23" />
35 <param name="maxquery" value="29" />
36 <param name="mintarget" value="23" />
37 <param name="maxtarget" value="29" />
38 <param name="overlap" value="10" />
39 <output file="paired.fa" ftype="fasta" name="output" />
40 </test>
41 </tests>
42 <help>
43
44 **What it does**
45
46 Extract reads with overlap signatures of the specified overlap (in nt) and
47 return a fasta file of these "pairable" reads.
48
49 See `Antoniewski (2014)`_ for background and details
50
51 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
52
53 **Input**
54
55 A **sorted** BAM alignment file.
56
57 **Outputs**
58
59 a fasta file of pairable reads such as :
60
61 >FBgn0000004_17.6|5839|R|26
62
63 TTTTCGTCAATTGTGCCAAATAGGTA
64
65 >FBgn0000004_17.6|5855|F|23
66
67 TTGACGAAAATGATCGAGTGGAT
68
69 where FBgn0000004_17.6 stands for the chromosome, 5839 stands for the 1-based read position,
70 R stand for reverse strand (F forward strand) and 26 stands for the size of the read.
71
72 the second sequence in this example is a read that overlap by 10 nt with the first read.
73
74 </help>
75 <citations>
76 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
77 </citations>
78 </tool>