root/galaxy-central/tools/fastx_toolkit/fastx_reverse_complement.xml

リビジョン 2, 1.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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</command>
5        <inputs>
6                <param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
7        </inputs>
8
9        <tests>
10                <test>
11                        <!-- Reverse-complement a FASTA file -->
12                        <param name="input" value="fastx_rev_comp1.fasta" />
13                        <output name="output" file="fastx_reverse_complement1.out" />
14                </test>
15                <test>
16                        <!-- Reverse-complement a FASTQ file -->
17                        <param name="input" value="fastx_rev_comp2.fastq" />
18                        <output name="output" file="fastx_reverse_complement2.out" />
19                </test>
20        </tests>
21
22 
23        <outputs>
24                <data format="input" name="output" metadata_source="input" />
25        </outputs>
26
27<help>
28**What it does**
29
30This tool reverse-complements each sequence in a library.
31If the library is a FASTQ, the quality-scores are also reversed.
32 
33--------
34
35**Example**
36
37Input FASTQ file::
38
39    @CSHL_1_FC42AGWWWXX:8:1:3:740
40    TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
41    +CSHL_1_FC42AGWWWXX:8:1:3:740
42    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
43
44
45Output FASTQ file::
46
47    @CSHL_1_FC42AGWWWXX:8:1:3:740
48    TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
49    +CSHL_1_FC42AGWWWXX:8:1:3:740
50    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
51
52------
53
54This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
55
56 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
57 
58</help>
59</tool>
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