Mercurial > repos > iuc > hyphy_strike_ambigs
comparison hyphy_strike_ambigs.xml @ 0:7c86ceaf523c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:27:46 +0000 |
| parents | |
| children | dc8875a13914 |
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| -1:000000000000 | 0:7c86ceaf523c |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@VERSION@"> | |
| 3 <description>in a multiple alignment using HyPhy</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 hyphy '$__tool_directory__/scripts/strike-ambigs.bf' | |
| 10 --alignment '$alignment' --output '$output' | |
| 11 @ERRORS@ | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param name="alignment" type="data" format="fasta" label="Input alignment" /> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="output" format="fasta" /> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="alignment" ftype="fasta" value="strike-ambigs-in1.fa"/> | |
| 22 <output name="output" file="strike-ambigs-out1.fa" /> | |
| 23 </test> | |
| 24 <test> | |
| 25 <param name="alignment" ftype="fasta" value="strike-ambigs-in2.fa"/> | |
| 26 <output name="output" file="strike-ambigs-out2.fa" /> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 HyPhy Strike-Ambigs | |
| 31 =================== | |
| 32 | |
| 33 Reads an alignment of coding sequences and replaces any ambiguous codons with ---. | |
| 34 | |
| 35 Note: The input fasta must be aligned along codon boundaries. | |
| 36 ]]></help> | |
| 37 <expand macro="citations"> | |
| 38 <citation type="doi">10.1093/bioinformatics/bti079</citation> | |
| 39 </expand> | |
| 40 </tool> |