Mercurial > repos > iuc > hyphy_conv
comparison hyphy_conv.xml @ 0:6a19eda9b9cb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:20:24 +0000 |
| parents | |
| children | 5d89d7b76ca7 |
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| -1:000000000000 | 0:6a19eda9b9cb |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy0" profile="19.09"> | |
| 3 <description>translate an in-frame codon alignment to proteins</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 cp '$input_file' conv_input.fa && | |
| 10 hyphy conv | |
| 11 '$gencodeid' | |
| 12 '$deletions' | |
| 13 conv_input.fa | |
| 14 aa.nhx | |
| 15 > ./conv.log | |
| 16 @ERRORS@ | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param name="input_file" type="data" format="fasta" label="Input codon alignment"/> | |
| 20 <param name="save_log" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Save the conversion log to your history" /> | |
| 21 <expand macro="gencode"/> | |
| 22 <param name="deletions" type="boolean" truevalue="Keep Deletions" falsevalue="Skip Deletions" label="Keep deletions" help="If this is checked, deletions will be left in the output file"/> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="conv_log" format="txt" from_work_dir="conv.log"> | |
| 26 <filter>save_log</filter> | |
| 27 </data> | |
| 28 <data name="proteins" format="nhx" from_work_dir="aa.nhx" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input_file" ftype="fasta" value="conv-in1.fa"/> | |
| 33 <param name="deletions" value="Keep Deletions" /> | |
| 34 <output name="proteins" file="conv-out1.nhx" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[ | |
| 38 HyPhy-CONV: Translate an in-frame codon alignment to proteins | |
| 39 ============================================================= | |
| 40 | |
| 41 This tool takes a codon-aligned fasta file and outputs the amino acid sequence | |
| 42 it represents, with the option to keep or skip deletions in the input file. | |
| 43 ]]> | |
| 44 </help> | |
| 45 <expand macro="citations" /> | |
| 46 </tool> | |
| 47 |