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

リビジョン 2, 1.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
37This tool converts RNA FASTA files to DNA (and vice-versa).
38
39In **RNA-to-DNA** mode, U's are changed into T's.
40
41In **DNA-to-RNA** mode, T's are changed into U's.
42
43--------
44
45**Example**
46
47Input 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
56Output 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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。