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comparison fasta_nucleotide_changer.xml @ 0:399fe8a8ce37

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author devteam
date Tue, 20 Aug 2013 10:17:35 -0400
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1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" >
2 <description>converter</description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f '$input' | fasta_nucleotide_changer -$mode -v -o $output</command>
7 <inputs>
8 <param format="fasta" version="1.0.0" name="input" type="data" label="Library to convert" />
9
10 <param version="1.0.0" name="mode" type="select" label="Convert">
11 <option value="d">RNA to DNA (U to T)</option>
12 <option value="r">DNA to RNA (T to U)</option>
13 </param>
14 </inputs>
15
16 <!--
17 Functional tests with param value starting with - fail.
18 -->
19 <tests>
20 <test>
21 <param version="1.0.0" name="input" value="fasta_nuc_changer1.fasta" />
22 <param version="1.0.0" name="mode" value="r" />
23 <output version="1.0.0" name="output" file="fasta_nuc_change1.out" />
24 </test>
25 <test>
26 <param version="1.0.0" name="input" value="fasta_nuc_changer2.fasta" />
27 <param version="1.0.0" name="mode" value="d" />
28 <output version="1.0.0" name="output" file="fasta_nuc_change2.out" />
29 </test>
30 </tests>
31
32 <outputs>
33 <data format="input" version="1.0.0" name="output" metadata_source="input" />
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
70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
71
72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
73
74 </help>
75 </tool>