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comparison fastx_reverse_complement.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
2 <description></description>
3 <command>
4 cat '$input' |
5 fastx_reverse_complement
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 -v -o '$output'
12 </command>
13 <inputs>
14 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
15 </inputs>
16
17 <tests>
18 <test>
19 <!-- Reverse-complement a FASTA file -->
20 <param name="input" value="fastx_rev_comp1.fasta" />
21 <output name="output" file="fastx_reverse_complement1.out" />
22 </test>
23 <test>
24 <!-- Reverse-complement a FASTQ file -->
25 <param name="input" value="fastx_rev_comp2.fastq" />
26 <output name="output" file="fastx_reverse_complement2.out" />
27 </test>
28 </tests>
29
30 <outputs>
31 <data format="input" name="output" metadata_source="input"
32 />
33 </outputs>
34
35 <help>
36 **What it does**
37
38 This tool reverse-complements each sequence in a library.
39 If the library is a FASTQ, the quality-scores are also reversed.
40
41 --------
42
43 **Example**
44
45 Input FASTQ file::
46
47 @CSHL_1_FC42AGWWWXX:8:1:3:740
48 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
49 +CSHL_1_FC42AGWWWXX:8:1:3:740
50 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
51
52
53 Output FASTQ file::
54
55 @CSHL_1_FC42AGWWWXX:8:1:3:740
56 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
57 +CSHL_1_FC42AGWWWXX:8:1:3:740
58 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
59
60 ------
61
62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
63
64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
65
66 </help>
67 </tool>
68 <!-- FASTX-reverse-complement is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->