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comparison seqtk_mergepe.xml @ 0:e0a0fd938de4 draft

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author iuc
date Thu, 05 Feb 2015 11:52:40 -0500
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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>