|
21
|
1
|
|
|
2 <!-- Flexbar tool definition for Galaxy, version 2.5 -->
|
|
|
3 <!-- Author: Johannes Roehr -->
|
|
|
4 <!-- Modified by Daniel Maticzka as specialized tool for splitting binary barcodes. -->
|
|
|
5
|
|
|
6
|
|
|
7 <tool id="flexbar_split_RR_bcs" name="Split by binary barcodes" version="2.5">
|
|
|
8
|
|
|
9 <description>using RR IUPAC pattern.</description>
|
|
|
10
|
|
|
11 <requirements>
|
|
|
12 <requirement type="package" version="2.5">flexbar</requirement>
|
|
|
13 </requirements>
|
|
|
14
|
|
|
15 <version_command>flexbar --version</version_command>
|
|
|
16
|
|
58
|
17 <command><![CDATA[
|
|
21
|
18
|
|
|
19 flexbar
|
|
|
20
|
|
|
21 --threads \${GALAXY_SLOTS:-1}
|
|
|
22
|
|
|
23 --reads $reads
|
|
|
24
|
|
|
25 --reads2 $reads2
|
|
|
26
|
|
|
27 #if $reads.ext == "fastqsanger":
|
|
|
28 --format sanger
|
|
|
29 #end if
|
|
|
30 #if $reads.ext == "fastqsolexa":
|
|
|
31 --format solexa
|
|
|
32 #end if
|
|
|
33 #if $reads.ext == "fastqillumina":
|
|
|
34 --format i1.3
|
|
|
35 #end if
|
|
|
36 #if $reads.ext == "csfasta":
|
|
|
37 --color-space
|
|
|
38 #end if
|
|
|
39 #if $reads.ext == "fastqcssanger":
|
|
|
40 --color-space
|
|
|
41 #end if
|
|
|
42
|
|
|
43 --barcodes $__tool_directory__/RR_bcs.fa
|
|
|
44
|
|
|
45 --barcode-reads $bReads
|
|
|
46
|
|
|
47 --barcode-threshold $bThresh
|
|
|
48
|
|
|
49 --max-uncalled $maxUncalled
|
|
|
50 --min-read-length $minReadLen
|
|
|
51
|
|
58
|
52 > $output
|
|
21
|
53
|
|
58
|
54 && mv flexbar_barcode_repA_1.fastq $output_repA_1
|
|
|
55 && mv flexbar_barcode_repA_2.fastq $output_repA_2
|
|
|
56 && mv flexbar_barcode_repB_1.fastq $output_repB_1
|
|
|
57 && mv flexbar_barcode_repB_2.fastq $output_repB_2
|
|
21
|
58
|
|
58
|
59 && sleep 20
|
|
|
60
|
|
|
61 ]]></command>
|
|
21
|
62
|
|
|
63
|
|
|
64 <inputs>
|
|
|
65
|
|
|
66 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
|
|
|
67
|
|
|
68 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
|
|
|
69
|
|
|
70 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
|
|
|
71
|
|
|
72 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
|
|
|
73
|
|
|
74 <param name="maxUncalled" size="4" type="integer" value="0" label="Max uncalled" optional="false" help="allowed uncalled bases per read"/>
|
|
|
75
|
|
|
76 <param name="minReadLen" size="4" type="integer" value="18" label="Minimum read length" optional="false" help="shorter reads are discarded"/>
|
|
|
77
|
|
|
78 </inputs>
|
|
|
79
|
|
|
80 <stdio>
|
|
|
81 <exit_code range="1:" level="fatal" description="Error!" />
|
|
|
82 </stdio>
|
|
|
83
|
|
|
84 <outputs>
|
|
|
85 <data format="txt" name="output" metadata_source="reads"/>
|
|
|
86 <data format="fastq" name="output_repA_1"/>
|
|
|
87 <data format="fastq" name="output_repA_2"/>
|
|
|
88 <data format="fastq" name="output_repB_1"/>
|
|
|
89 <data format="fastq" name="output_repB_2"/>
|
|
|
90 </outputs>
|
|
|
91
|
|
|
92
|
|
|
93 <help>
|
|
|
94
|
|
|
95 **Description**
|
|
|
96
|
|
|
97 This tool splits paired-end reads according to an external set of barcode reads in RY IUPAC format according to patterns RR (replicate A) and YY (replicate B) using Flexbar.
|
|
|
98
|
|
|
99 .. _project: https://github.com/seqan/flexbar
|
|
|
100
|
|
|
101 ------
|
|
|
102
|
|
|
103 **Reference**
|
|
|
104
|
|
|
105 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
|
|
|
106
|
|
|
107 </help>
|
|
|
108
|
|
|
109 </tool>
|
