Mercurial > repos > devteam > fasta_nucleotide_changer

comparison fasta_nucleotide_changer.xml @ 2:f81d4362b6c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Mon, 12 Oct 2015 10:18:10 -0400
parents 2f868bfbe9de
children cc9a18dd41c9
comparison
equal deleted inserted replaced
1:2f868bfbe9de 2:f81d4362b6c1
1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" > 1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" >
2 <description>converter</description> 2 <description>converter</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command>zcat -f '$input' | fasta_nucleotide_changer -$mode -v -o $output</command> 6 <command>
7 <inputs> 7 <![CDATA[
8 <param format="fasta" name="input" type="data" label="Library to convert" /> 8 zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output'
9 ]]>
10 </command>
11 <inputs>
12 <param format="fasta" name="input" type="data" label="Library to convert" />
9 13
10 <param name="mode" type="select" label="Convert"> 14 <param name="mode" type="select" label="Convert">
11 <option value="d">RNA to DNA (U to T)</option> 15 <option value="d">RNA to DNA (U to T)</option>
12 <option value="r">DNA to RNA (T to U)</option> 16 <option value="r">DNA to RNA (T to U)</option>
13 </param> 17 </param>
14 </inputs> 18 </inputs>
15 19 <outputs>
16 <!-- 20 <data format_source="input" name="output" metadata_source="input" />
17 Functional tests with param value starting with - fail. 21 </outputs>
18 --> 22 <tests>
19 <tests> 23 <test>
20 <test> 24 <param name="input" value="fasta_nuc_changer1.fasta" />
21 <param name="input" value="fasta_nuc_changer1.fasta" /> 25 <param name="mode" value="r" />
22 <param name="mode" value="r" /> 26 <output name="output" ftype="fasta" file="fasta_nuc_change1.out" />
23 <param name="output" file="fasta_nuc_change1.out" /> 27 </test>
24 </test> 28 <test>
25 <test> 29 <param name="input" value="fasta_nuc_changer2.fasta" />
26 <param name="input" value="fasta_nuc_changer2.fasta" /> 30 <param name="mode" value="d" />
27 <param name="mode" value="d" /> 31 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
28 <param name="output" file="fasta_nuc_change2.out" /> 32 </test>
29 </test> 33 </tests>
30 </tests> 34 <help>
31
32 <outputs>
33 <data format="input" name="output" metadata_source="input" />
34 </outputs>
35
36 <help>
37 **What it does** 35 **What it does**
38 36
39 This tool converts RNA FASTA files to DNA (and vice-versa). 37 This tool converts RNA FASTA files to DNA (and vice-versa).
40 38
41 In **RNA-to-DNA** mode, U's are changed into T's. 39 In **RNA-to-DNA** mode, U's are changed into T's.
68 ------ 66 ------
69 67
70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
71 69
72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
73 71 </help>
74 </help>
75 </tool> 72 </tool>