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comparison tools/fastx_toolkit/fastx_reverse_complement.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
2 <description></description>
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4 <command>zcat -f '$input' | fastx_reverse_complement -v -o $output
5 #if $input.ext == "fastqsanger":
6 -Q 33
7 #end if
8 </command>
9 <inputs>
10 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
11 </inputs>
12
13 <tests>
14 <test>
15 <!-- Reverse-complement a FASTA file -->
16 <param name="input" value="fastx_rev_comp1.fasta" />
17 <output name="output" file="fastx_reverse_complement1.out" />
18 </test>
19 <test>
20 <!-- Reverse-complement a FASTQ file -->
21 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
22 <output name="output" file="fastx_reverse_complement2.out" />
23 </test>
24 </tests>
25
26
27 <outputs>
28 <data format="input" name="output" metadata_source="input" />
29 </outputs>
30
31 <help>
32 **What it does**
33
34 This tool reverse-complements each sequence in a library.
35 If the library is a FASTQ, the quality-scores are also reversed.
36
37 --------
38
39 **Example**
40
41 Input FASTQ file::
42
43 @CSHL_1_FC42AGWWWXX:8:1:3:740
44 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
45 +CSHL_1_FC42AGWWWXX:8:1:3:740
46 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
47
48
49 Output FASTQ file::
50
51 @CSHL_1_FC42AGWWWXX:8:1:3:740
52 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
53 +CSHL_1_FC42AGWWWXX:8:1:3:740
54 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
55
56 ------
57
58 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
59
60 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
61
62 </help>
63 </tool>