Mercurial > repos > iuc > hyphy_conv
comparison hyphy_conv.xml @ 1:c1d24ff838c8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
author | iuc |
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date | Tue, 20 Apr 2021 19:55:16 +0000 |
parents | 9ce3d6d4bd0e |
children | f6e7b5955712 |
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0:9ce3d6d4bd0e | 1:c1d24ff838c8 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy0" profile="19.09"> | 2 <tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy1" profile="19.09"> |
3 <description>translate an in-frame codon alignment to proteins</description> | 3 <description>translate an in-frame codon alignment to proteins</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"/> |
9 cp '$input_file' conv_input.fa && | 9 cp '$input_file' conv_input.fa && |
10 hyphy conv | 10 hyphy conv |
11 '$gencodeid' | 11 '$gencodeid' |
12 '$deletions' | 12 '$deletions' |
13 conv_input.fa | 13 conv_input.fa |
14 aa.nhx | 14 aa.nex |
15 > ./conv.log | 15 > ./conv.log |
16 @ERRORS@ | 16 @ERRORS@ |
17 ]]></command> | 17 ]]></command> |
18 <inputs> | 18 <inputs> |
19 <param name="input_file" type="data" format="fasta" label="Input codon alignment"/> | 19 <param name="input_file" type="data" format="fasta" label="Input codon alignment"/> |
23 </inputs> | 23 </inputs> |
24 <outputs> | 24 <outputs> |
25 <data name="conv_log" format="txt" from_work_dir="conv.log"> | 25 <data name="conv_log" format="txt" from_work_dir="conv.log"> |
26 <filter>save_log</filter> | 26 <filter>save_log</filter> |
27 </data> | 27 </data> |
28 <data name="proteins" format="nhx" from_work_dir="aa.nhx" /> | 28 <data name="proteins" format="nex" from_work_dir="aa.nex" /> |
29 </outputs> | 29 </outputs> |
30 <tests> | 30 <tests> |
31 <test> | 31 <test> |
32 <param name="input_file" ftype="fasta" value="conv-in1.fa"/> | 32 <param name="input_file" ftype="fasta" value="conv-in1.fa"/> |
33 <param name="deletions" value="Keep Deletions" /> | 33 <param name="deletions" value="Keep Deletions" /> |
34 <output name="proteins" file="conv-out1.nhx" /> | 34 <output name="proteins" file="conv-out1.nex" /> |
35 </test> | 35 </test> |
36 </tests> | 36 </tests> |
37 <help><![CDATA[ | 37 <help><![CDATA[ |
38 HyPhy-CONV: Translate an in-frame codon alignment to proteins | 38 HyPhy-CONV: Translate an in-frame codon alignment to proteins |
39 ============================================================= | 39 ============================================================= |