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comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastx_reverse_complement.xml @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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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
29 This tool reverse-complements each sequence in a library.
30 If the library is a FASTQ, the quality-scores are also reversed.
31
32 --------
33
34 **Example**
35
36 Input 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
44 Output 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>