Mercurial > repos > iuc > hyphy_conv

comparison hyphy_conv.xml @ 1:5d89d7b76ca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
author iuc
date Tue, 20 Apr 2021 19:44:05 +0000
parents 6a19eda9b9cb
children 67edc6d534c3
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0:6a19eda9b9cb 1:5d89d7b76ca7
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 =============================================================