|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0">
|
|
|
3 <description>interleave two unpaired FASTA/Q files for a paired-end file</description>
|
|
|
4 <macros>
|
|
|
5 <import>macros.xml</import>
|
|
|
6 </macros>
|
|
|
7 <expand macro="requirements"/>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <command><![CDATA[seqtk mergepe
|
|
|
10 $in_fq1
|
|
|
11 $in_fq2
|
|
|
12 > $default]]></command>
|
|
|
13 <inputs>
|
|
|
14 <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
|
|
|
15 <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
|
|
|
16 </inputs>
|
|
|
17 <outputs>
|
|
|
18 <data format_source="in_fq1" hidden="false" name="default" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
|
|
|
19 </outputs>
|
|
|
20 <tests>
|
|
|
21 <test>
|
|
|
22 <param name="in_fq1" value="paired_dat1.fq"/>
|
|
|
23 <param name="in_fq2" value="paired_dat2.fq"/>
|
|
|
24 <output name="default" file="paired_dat.fq" ftype="fastq"/>
|
|
|
25 </test>
|
|
|
26 </tests>
|
|
|
27 <help><![CDATA[
|
|
|
28 **What it does**
|
|
|
29
|
|
|
30 Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
|
|
|
31
|
|
|
32 ::
|
|
|
33
|
|
|
34 # r1.fq
|
|
|
35 @test-6/1
|
|
|
36 AGCTTGACGC
|
|
|
37 +
|
|
|
38 ?.HCF@C>>F
|
|
|
39
|
|
|
40 # r2.fq
|
|
|
41 @test-6/2
|
|
|
42 TGCGAAGACC
|
|
|
43 +
|
|
|
44 >2?A?A@@7?
|
|
|
45
|
|
|
46 will produce the following paired file:
|
|
|
47
|
|
|
48 ::
|
|
|
49
|
|
|
50 @test-6/1
|
|
|
51 AGCTTGACGC
|
|
|
52 +
|
|
|
53 ?.HCF@C>>F
|
|
|
54 @test-6/2
|
|
|
55 TGCGAAGACC
|
|
|
56 +
|
|
|
57 >2?A?A@@7?
|
|
|
58
|
|
|
59 While this may not have been an illuminating example, it is important to note
|
|
|
60 that this tool will properly interleave data. For example if you have the ids:
|
|
|
61
|
|
|
62 ::
|
|
|
63
|
|
|
64 @r-1/1
|
|
|
65 @r-2/1
|
|
|
66 @r-3/1
|
|
|
67 @r-4/1
|
|
|
68
|
|
|
69 and
|
|
|
70
|
|
|
71 ::
|
|
|
72
|
|
|
73 @r-1/2
|
|
|
74 @r-2/2
|
|
|
75 @r-3/2
|
|
|
76 @r-4/2
|
|
|
77
|
|
|
78 These will be interleaved as
|
|
|
79
|
|
|
80 ::
|
|
|
81
|
|
|
82 @r-1/1
|
|
|
83 @r-1/2
|
|
|
84 @r-2/1
|
|
|
85 @r-2/2
|
|
|
86 @r-3/1
|
|
|
87 @r-3/2
|
|
|
88 @r-4/1
|
|
|
89 @r-4/2
|
|
|
90
|
|
|
91 @ATTRIBUTION@
|
|
|
92 ]]></help>
|
|
|
93 </tool>
|
