Mercurial > repos > peterjc > align_back_trans

comparison tools/align_back_trans/align_back_trans.xml @ 6:b27388e5a0bb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.0.10 removed unused reference to muscle format
author peterjc
date Mon, 21 Aug 2017 06:26:14 -0400
parents 2c32e8a8990f
children 883842b81796
comparison
equal deleted inserted replaced
5:2c32e8a8990f 6:b27388e5a0bb
1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.9"> 1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.10">
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="1.67">biopython</requirement> 4 <requirement type="package" version="1.67">biopython</requirement>
5 </requirements> 5 </requirements>
6 <version_command> 6 <version_command>
7 python $__tool_directory__/align_back_trans.py --version 7 python $__tool_directory__/align_back_trans.py --version
8 </version_command> 8 </version_command>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 python $__tool_directory__/align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table' 10 python $__tool_directory__/align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table'
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." /> 13 <param name="prot_align" type="data" format="fasta,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
14 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> 14 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
15 <option value="1">1. Standard</option> 15 <option value="1">1. Standard</option>
16 <option value="2">2. Vertebrate Mitochondrial</option> 16 <option value="2">2. Vertebrate Mitochondrial</option>
17 <option value="3">3. Yeast Mitochondrial</option> 17 <option value="3">3. Yeast Mitochondrial</option>
18 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> 18 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>