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comparison seqtk_mutfa.xml @ 4:8a5151868549 draft

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author iuc
date Wed, 29 Apr 2015 12:07:03 -0400
parents 33ded39275c3
children 55e75a28fde7
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3:e7d27bcef53d 4:8a5151868549
1 <?xml version="1.0"?>
2 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
3 <description>point mutate FASTA at specified positions</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk mutfa
10 $in_file $in_snp
11 > $default]]></command>
12 <inputs>
13 <expand macro="in_faq"/>
14 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
15 </inputs>
16 <outputs>
17 <data format_source="in_file" hidden="false" name="default" label="Mutated $in_file.name"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="in_file" value="seqtk_mutfa.fa"/>
22 <param name="in_snp" value="seqtk_mutfa.snp"/>
23 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
24 </test>
25 </tests>
26 <help><![CDATA[
27 **What it does**
28
29 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
30
31 ::
32
33 # Input fasta
34 >test0
35 ACTGACTGAA
36
37 # Input SNP file
38 test0 1 . G
39 test0 4 . A
40
41 This will effect the desired mutations in the output file
42
43 ::
44
45 # Output result
46 >test0
47 GCTAACTGAA
48
49 @ATTRIBUTION@
50 ]]></help>
51 </tool>