Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/format_fasta.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
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date | Sat, 21 Apr 2012 21:36:15 -0400 |
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0:d50638ebd809 | 1:8593828f91e7 |
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1 <tool id="rtg_format_fasta" name="Format FASTA"> | |
2 <description>to SDF with rtg format</description> | |
3 <command interpreter="bash">galaxy-rtg-wrapper.sh format | |
4 #if $paired.sPaired == "paired": | |
5 -l $paired.input1 | |
6 -r $paired.input2 | |
7 #else: | |
8 $paired.input1 | |
9 #end if | |
10 #if str($protein) == "true": | |
11 -p | |
12 #end if | |
13 -o ${output.extra_files_path} >$output</command> | |
14 <inputs> | |
15 <conditional name="paired"> | |
16 <param name="sPaired" type="select" label="Are you formatting paired-end reads?"> | |
17 <option value="single">Non-read data or single-end</option> | |
18 <option value="paired">Paired-end</option> | |
19 </param> | |
20 <when value="single"> | |
21 <param name="input1" type="data" format="fasta" label="Source FASTA file"/> | |
22 </when> | |
23 <when value="paired"> | |
24 <param name="input1" type="data" format="fasta" label="First of pair FASTA file"/> | |
25 <param name="input2" type="data" format="fasta" label="Second of pairFASTA file"/> | |
26 </when> | |
27 </conditional> | |
28 <param name="protein" type="select" label="Input consists of protein"> | |
29 <option value="false" selected="true">False</option> | |
30 <option value="true">True</option> | |
31 </param> | |
32 </inputs> | |
33 <outputs> | |
34 <data format="rtg_sdf" name="output" /> | |
35 </outputs> | |
36 | |
37 <help> | |
38 This tool formats a FASTA file to RTG SDF. | |
39 </help> | |
40 | |
41 </tool> |