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comparison seqtk_mutfa.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
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2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
3 <description>point mutate FASTA at specified positions</description> 3 <description>point mutate FASTA at specified positions</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk mutfa 9 <command><![CDATA[
10 $in_file $in_snp 10 seqtk mutfa
11 > $default]]></command> 11 '$in_file'
12 <inputs> 12 '$in_snp'
13 <expand macro="in_faq"/> 13 > '$default'
14 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/> 14 ]]></command>
15 </inputs> 15 <inputs>
16 <outputs> 16 <expand macro="in_faq"/>
17 <data format_source="in_file" hidden="false" name="default" label="Mutated $in_file.name"/> 17 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
18 </outputs> 18 </inputs>
19 <tests> 19 <outputs>
20 <test> 20 <data name="default" format_source="in_file" label="Mutated $in_file.name"/>
21 <param name="in_file" value="seqtk_mutfa.fa"/> 21 </outputs>
22 <param name="in_snp" value="seqtk_mutfa.snp"/> 22 <tests>
23 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/> 23 <test>
24 </test> 24 <param name="in_file" value="seqtk_mutfa.fa"/>
25 </tests> 25 <param name="in_snp" value="seqtk_mutfa.snp"/>
26 <help><![CDATA[ 26 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
27 </test>
28 </tests>
29 <help><![CDATA[
27 **What it does** 30 **What it does**
28 31
29 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to. 32 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
30 33
31 :: 34 ::
45 # Output result 48 # Output result
46 >test0 49 >test0
47 GCTAACTGAA 50 GCTAACTGAA
48 51
49 @ATTRIBUTION@ 52 @ATTRIBUTION@
50 ]]></help> 53 ]]></help>
51 <expand macro="citation" /> 54 <expand macro="citation" />
52 </tool> 55 </tool>