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author devteam
date Wed, 25 Sep 2013 11:20:25 -0400
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1 <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f '$input' | fastx_reverse_complement -v -o $output
7 #if $input.ext == "fastqsanger":
8 -Q 33
9 #end if
10 </command>
11 <inputs>
12 <param format="fasta,fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to reverse-complement" />
13 </inputs>
14
15 <tests>
16 <test>
17 <!-- Reverse-complement a FASTA file -->
18 <param version="1.0.0" name="input" value="fastx_rev_comp1.fasta" />
19 <output version="1.0.0" name="output" file="fastx_reverse_complement1.out" />
20 </test>
21 <test>
22 <!-- Reverse-complement a FASTQ file -->
23 <param version="1.0.0" name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
24 <output version="1.0.0" name="output" file="fastx_reverse_complement2.out" />
25 </test>
26 </tests>
27
28
29 <outputs>
30 <data format="input" version="1.0.0" name="output" metadata_source="input" />
31 </outputs>
32
33 <help>
34 **What it does**
35
36 This tool reverse-complements each sequence in a library.
37 If the library is a FASTQ, the quality-scores are also reversed.
38
39 --------
40
41 **Example**
42
43 Input FASTQ file::
44
45 @CSHL_1_FC42AGWWWXX:8:1:3:740
46 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
47 +CSHL_1_FC42AGWWWXX:8:1:3:740
48 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
49
50
51 Output FASTQ file::
52
53 @CSHL_1_FC42AGWWWXX:8:1:3:740
54 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
55 +CSHL_1_FC42AGWWWXX:8:1:3:740
56 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
57
58 ------
59
60 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
61
62 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
63
64 </help>
65 </tool>