Mercurial > repos > peterjc > align_back_trans

comparison tools/align_back_trans/align_back_trans.xml @ 1:ec202446408a draft

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Uploaded v0.0.4, fixed an error message.
author peterjc
date Wed, 04 Jun 2014 08:42:23 -0400
parents 0c24e4e2177d
children 9fbf29a8c12b
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0:0c24e4e2177d 1:ec202446408a
1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.3"> 1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.4">
2 <description>Gives a codon aware alignment</description> 2 <description>Gives a codon aware alignment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.63">biopython</requirement> 4 <requirement type="package" version="1.63">biopython</requirement>
5 <requirement type="python-module">Bio</requirement> 5 <requirement type="python-module">Bio</requirement>
6 </requirements> 6 </requirements>
36 <option value="0">Don't check the translation</option> 36 <option value="0">Don't check the translation</option>
37 </param> 37 </param>
38 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> 38 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="out_nuc_align" format="fasta" label="${prot_align.name} (back-translated)"> 41 <data name="out_nuc_align" format="input" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
42 <!-- TODO - Replace this with format="input:prot_align" if/when that works -->
43 <change_format>
44 <when input_dataset="prot_align" attribute="extension" value="clustal" format="clustal" />
45 <when input_dataset="prot_align" attribute="extension" value="phylip" format="phylip" />
46 </change_format>
47 </data>
48 </outputs> 42 </outputs>
49 <tests> 43 <tests>
50 <test> 44 <test>
51 <param name="prot_align" value="demo_prot_align.fasta" /> 45 <param name="prot_align" value="demo_prot_align.fasta" />
52 <param name="nuc_file" value="demo_nucs.fasta" /> 46 <param name="nuc_file" value="demo_nucs.fasta" />