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comparison seqtk_dropse.xml @ 6:113f3c3d6bee draft

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author iuc
date Wed, 29 Apr 2015 22:47:00 -0400
parents 33ded39275c3
children 55e75a28fde7
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5:fd11d2328ca8 6:113f3c3d6bee
1 <?xml version="1.0"?>
2 <tool id="seqtk_dropse" name="seqtk_dropse" version="@WRAPPER_VERSION@.0">
3 <description>drop unpaired from interleaved Paired End FASTA/Q</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk dropse
10 $in_file
11 > $default]]></command>
12 <inputs>
13 <expand macro="in_faq"/>
14 </inputs>
15 <outputs>
16 <data format_source="in_file" hidden="false" name="default" label="Only paired-end reads from $in_file.name"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="in_file" value="seqtk_dropse.fq"/>
21 <output name="default" file="seqtk_dropse.out" ftype="fastq"/>
22 </test>
23 </tests>
24 <help><![CDATA[
25 **What it does**
26
27 Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:
28
29 ::
30
31 @test-6/1
32 AGCTTGACGC
33 +
34 ?.HCF@C>>F
35 @test-6/2
36 TGCGAAGACC
37 +
38 >2?A?A@@7?
39 @test-4/1
40 CTTGACGCTG
41 +
42 I@>3EFCG@C
43 @test-2/1
44 AGACCAAAAT
45 +
46 ??><6E?IFC
47 @test-2/2
48 CTGGCGAATT
49 +
50 ?=?*?A?<?@
51
52 This tool will remove the offending reads (test-4/1), leaving just the paired data.
53
54 ::
55
56 @test-6/1
57 AGCTTGACGC
58 +
59 ?.HCF@C>>F
60 @test-6/2
61 TGCGAAGACC
62 +
63 >2?A?A@@7?
64 @test-2/1
65 AGACCAAAAT
66 +
67 ??><6E?IFC
68 @test-2/2
69 CTGGCGAATT
70 +
71 ?=?*?A?<?@
72
73
74 @ATTRIBUTION@
75 ]]></help>
76 </tool>