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comparison fasta_nucleotide_changer.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_fasta_nucleotides_changer" name="RNA/DNA" >
2 <description>converter</description>
3 <command>
4 cat '$input' |
5 fasta_nucleotide_changer $mode -v -o '$output'</command>
6 <inputs>
7 <param format="fasta" name="input" type="data" label="Library to convert" />
8
9 <param name="mode" type="select" label="Convert">
10 <option value="-d">RNA to DNA (U to T)</option>
11 <option value="-r">DNA to RNA (T to U)</option>
12 </param>
13 </inputs>
14
15 <tests>
16 <test>
17 <!-- DNA-to-RNA -->
18 <param name="input" value="fasta_nuc_changer1.fasta" />
19 <param name="mode" value="DNA to RNA (T to U)" />
20 <output name="output" file="fasta_nuc_changer1.out" />
21 </test>
22 <test>
23 <!-- RNA-to-DNA -->
24 <param name="input" value="fasta_nuc_changer2.fasta" />
25 <param name="mode" value="RNA to DNA (U to T)" />
26 <output name="output" file="fasta_nuc_changer2.out" />
27 </test>
28 </tests>
29
30
31 <outputs>
32 <data format="input" name="output" metadata_source="input"
33 />
34 </outputs>
35
36 <help>
37 **What it does**
38
39 This tool converts RNA FASTA files to DNA (and vice-versa).
40
41 In **RNA-to-DNA** mode, U's are changed into T's.
42
43 In **DNA-to-RNA** mode, T's are changed into U's.
44
45 --------
46
47 **Example**
48
49 Input RNA FASTA file ( from Sanger's mirBase )::
50
51 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
52 UGAGGUAGUAGGUUGUAUAGUU
53 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
54 UCCCUGAGACCUCAAGUGUGA
55 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
56 UGGAAUGUAAAGAAGUAUGUA
57
58 Output DNA FASTA file (with RNA-to-DNA mode)::
59
60 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
61 TGAGGTAGTAGGTTGTATAGTT
62 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
63 TCCCTGAGACCTCAAGTGTGA
64 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
65 TGGAATGTAAAGAAGTATGTA
66
67 ------
68
69 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
70
71 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
72 </help>
73 </tool>
74 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->