/tools/fastx_toolkit/fastx_reverse_complement.xml

 1<tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
 2	<description>sequences</description>
 3	<command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command>
 4	<inputs>
 5		<param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
 6	</inputs>
 7
 8	<tests>
 9		<test>
10			<!-- Reverse-complement a FASTA file -->
11			<param name="input" value="fastx_rev_comp1.fasta" /> 
12			<output name="output" file="fastx_reverse_complement1.out" />
13		</test>
14		<test>
15			<!-- Reverse-complement a FASTQ file -->
16			<param name="input" value="fastx_rev_comp2.fastq" />
17			<output name="output" file="fastx_reverse_complement2.out" />
18		</test>
19	</tests>
20
21  
22	<outputs>
23		<data format="input" name="output" metadata_source="input" />
24	</outputs>
25
26<help>
27**What it does**
28
29This tool reverse-complements each sequence in a library.
30If the library is a FASTQ, the quality-scores are also reversed.
31  
32--------
33
34**Example**
35
36Input FASTQ file::
37
38    @CSHL_1_FC42AGWWWXX:8:1:3:740
39    TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
40    +CSHL_1_FC42AGWWWXX:8:1:3:740
41    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
42
43
44Output FASTQ file::
45
46    @CSHL_1_FC42AGWWWXX:8:1:3:740
47    TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
48    +CSHL_1_FC42AGWWWXX:8:1:3:740
49    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
50
51</help>
52</tool>