Mercurial > repos > devteam > fasta_nucleotide_changer

comparison fasta_nucleotide_changer.xml @ 3:cc9a18dd41c9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:01 -0400
parents f81d4362b6c1
children 091ca73f5804
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2:f81d4362b6c1 3:cc9a18dd41c9
1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" > 1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.1" name="RNA/DNA" >
2 <description>converter</description> 2 <description>converter</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command> 6 <expand macro="requirements" />
7 <![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output' 8 @CATS@ fasta_nucleotide_changer
9 ]]> 9 -$mode
10 </command> 10 -v
11 -o '$output'
12 ]]></command>
11 <inputs> 13 <inputs>
12 <param format="fasta" name="input" type="data" label="Library to convert" /> 14 <expand macro="fasta_input" />
13 15
14 <param name="mode" type="select" label="Convert"> 16 <param name="mode" type="select" label="Convert">
15 <option value="d">RNA to DNA (U to T)</option> 17 <option value="d">RNA to DNA (U to T)</option>
16 <option value="r">DNA to RNA (T to U)</option> 18 <option value="r">DNA to RNA (T to U)</option>
17 </param> 19 </param>
18 </inputs> 20 </inputs>
19 <outputs> 21 <outputs>
20 <data format_source="input" name="output" metadata_source="input" /> 22 <data name="output" format_source="input" metadata_source="input" />
21 </outputs> 23 </outputs>
22 <tests> 24 <tests>
23 <test> 25 <test>
24 <param name="input" value="fasta_nuc_changer1.fasta" /> 26 <param name="input" value="fasta_nuc_changer1.fasta" />
25 <param name="mode" value="r" /> 27 <param name="mode" value="r" />
29 <param name="input" value="fasta_nuc_changer2.fasta" /> 31 <param name="input" value="fasta_nuc_changer2.fasta" />
30 <param name="mode" value="d" /> 32 <param name="mode" value="d" />
31 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" /> 33 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
32 </test> 34 </test>
33 </tests> 35 </tests>
34 <help> 36 <help><![CDATA[
35 **What it does** 37 **What it does**
36 38
37 This tool converts RNA FASTA files to DNA (and vice-versa). 39 This tool converts RNA FASTA files to DNA (and vice-versa).
38 40
39 In **RNA-to-DNA** mode, U's are changed into T's. 41 In **RNA-to-DNA** mode, U's are changed into T's.
66 ------ 68 ------
67 69
68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
69 71
70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
71 </help> 73 ]]></help>
74 <expand macro="citations" />
72 </tool> 75 </tool>