Mercurial > repos > iuc > hyphy_conv

comparison hyphy_conv.xml @ 12:71ef72fc6dc4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:43:38 +0000
parents 1fc726fccf7c
children
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11:1fc726fccf7c 12:71ef72fc6dc4
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 cp '$input_file' conv_input.fa && 8 cp '$input_file' conv_input.fa &&
9 hyphy conv 9 ENV="TOLERATE_NUMERICAL_ERRORS=1;" hyphy conv
10 '$gencodeid' 10 '$gencodeid'
11 '$deletions' 11 '$deletions'
12 conv_input.fa 12 conv_input.fa
13 aa.nex 13 aa.nex
14 @ERRORS@ 14 @ERRORS@
22 <data name="proteins" format="nex" from_work_dir="aa.nex" /> 22 <data name="proteins" format="nex" from_work_dir="aa.nex" />
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test> 25 <test>
26 <param name="input_file" ftype="fasta" value="conv-in1.fa"/> 26 <param name="input_file" ftype="fasta" value="conv-in1.fa"/>
27 <param name="deletions" value="Keep Deletions" /> 27 <param name="deletions" value="true" />
28 <output name="proteins" file="conv-out1.nex" /> 28 <output name="proteins" file="conv-out1.nex" />
29 </test> 29 </test>
30 </tests> 30 </tests>
31 <help><![CDATA[ 31 <help><![CDATA[
32 HyPhy-CONV: Translate an in-frame codon alignment to proteins 32 HyPhy-CONV: Translate an in-frame codon alignment to proteins