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comparison fa-extract-sequence.xml @ 5:21888a4371d1 draft default tip

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planemo upload for repository https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract commit df418d3445a03025bf38d27b1272fb913be548f1-dirty
author nml
date Wed, 20 Sep 2017 13:25:29 -0400
parents 0470423f5a47
children
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4:c96a4314df39 5:21888a4371d1
1 <tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.0.0"> 1 <tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.1.0">
2 <description>Extract a single sequence from a fasta file.</description> 2 <description>Extract a single sequence from a fasta file.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.22.2.1">perl</requirement>
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 </requirements> 5 </requirements>
7 <command interpreter="perl"> 6 <command >
8 fa-extract-few.pl 7 perl $__tool_directory__/fa-extract-few.pl
9 -f $dataset 8 -f $dataset
10 $exact 9 $exact
11 $inverse 10 $inverse
12 #if $file_or_type.select == "list" 11 #if $file_or_type.select == "list"
13 --list $file_or_type.list_file 12 --list $file_or_type.list_file
33 </when> 32 </when>
34 <when value="single"> 33 <when value="single">
35 <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." /> 34 <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." />
36 </when> 35 </when>
37 </conditional> 36 </conditional>
38
39
40 </inputs> 37 </inputs>
41 <outputs> 38 <outputs>
42 <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/> 39 <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/>
43 </outputs> 40 </outputs>
44 <tests> 41 <tests>
45 <test> 42 <test>
46 <output/> 43 <param name="dataset" value="input.fasta"/>
44 <param name="select" value="single"/>
45 <param name="id" value="B0R37_29930"/>
46 <output name="output" value="output.fasta"/>
47 </test> 47 </test>
48 </tests> 48 </tests>
49 <help> 49 <help>
50 **Fasta Extract Sequence** 50 **Fasta Extract Sequence**
51 Extracts a fasta sequence from a multfasta by id (exact or partial) 51 Extracts a fasta sequence from a multfasta by id (exact or partial)