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comparison tools/fastx_toolkit/fasta_nucleotide_changer.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cshl_fasta_nucleotides_changer" name="RNA/DNA" >
2 <description>converter</description>
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4 <command>zcat -f '$input' | fasta_nucleotide_changer $mode -v -o $output</command>
5 <inputs>
6 <param format="fasta" name="input" type="data" label="Library to convert" />
7
8 <param name="mode" type="select" label="Convert">
9 <option value="-d">RNA to DNA (U to T)</option>
10 <option value="-r">DNA to RNA (T to U)</option>
11 </param>
12 </inputs>
13
14 <!--
15 Functional tests with param value starting with - fail.
16 <tests>
17 <test>
18 <param name="input" value="fasta_nuc_changer1.fasta" />
19 <param name="mode" value="-r" />
20 <output name="output" file="fasta_nuc_change1.out" />
21 </test>
22 <test>
23 <param name="input" value="fasta_nuc_changer2.fasta" />
24 <param name="mode" value="-d" />
25 <output name="output" file="fasta_nuc_change2.out" />
26 </test>
27 </tests>
28 -->
29
30 <outputs>
31 <data format="input" name="output" metadata_source="input" />
32 </outputs>
33
34 <help>
35 **What it does**
36
37 This tool converts RNA FASTA files to DNA (and vice-versa).
38
39 In **RNA-to-DNA** mode, U's are changed into T's.
40
41 In **DNA-to-RNA** mode, T's are changed into U's.
42
43 --------
44
45 **Example**
46
47 Input RNA FASTA file ( from Sanger's mirBase )::
48
49 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
50 UGAGGUAGUAGGUUGUAUAGUU
51 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
52 UCCCUGAGACCUCAAGUGUGA
53 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
54 UGGAAUGUAAAGAAGUAUGUA
55
56 Output DNA FASTA file (with RNA-to-DNA mode)::
57
58 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
59 TGAGGTAGTAGGTTGTATAGTT
60 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
61 TCCCTGAGACCTCAAGTGTGA
62 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
63 TGGAATGTAAAGAAGTATGTA
64
65 </help>
66 </tool>