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comparison flexbar_split_RR_bcs.xml @ 21:25ebec14969a draft

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Add RR/YY binary splitting
author rnateam
date Fri, 11 Dec 2015 03:50:38 -0500
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children bbbae1ee87e0
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20:c17588f80c6f 21:25ebec14969a
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
17 <command>
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
52 > $output;
53
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;
58
59 </command>
60
61
62 <inputs>
63
64 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
65
66 <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"/>
67
68 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
69
70 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
71
72 <param name="maxUncalled" size="4" type="integer" value="0" label="Max uncalled" optional="false" help="allowed uncalled bases per read"/>
73
74 <param name="minReadLen" size="4" type="integer" value="18" label="Minimum read length" optional="false" help="shorter reads are discarded"/>
75
76 </inputs>
77
78 <stdio>
79 <exit_code range="1:" level="fatal" description="Error!" />
80 </stdio>
81
82 <outputs>
83 <data format="txt" name="output" metadata_source="reads"/>
84 <data format="fastq" name="output_repA_1"/>
85 <data format="fastq" name="output_repA_2"/>
86 <data format="fastq" name="output_repB_1"/>
87 <data format="fastq" name="output_repB_2"/>
88 </outputs>
89
90
91 <help>
92
93 **Description**
94
95 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.
96
97 .. _project: https://github.com/seqan/flexbar
98
99 ------
100
101 **Reference**
102
103 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.
104
105 </help>
106
107 </tool>