Mercurial > repos > iuc > seqtk
annotate seqtk_mutfa.xml @ 8:d3b46dec1f5e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e5a5ad091c621348dc6ce2df861475ebc54a380e
| author | iuc |
|---|---|
| date | Tue, 13 Oct 2015 17:27:35 -0400 |
| parents | 55e75a28fde7 |
| children | 16f2535c08bf |
| rev | line source |
|---|---|
| 0 | 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> | |
|
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55e75a28fde7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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51 <expand macro="citation" /> |
| 0 | 52 </tool> |