Mercurial > repos > peterjc > align_back_trans

comparison tools/align_back_trans/align_back_trans.xml @ 2:9fbf29a8c12b draft

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v0.0.6 use format_source; v0.0.5 more explicit error msg, citation info
author peterjc
date Wed, 05 Aug 2015 10:52:56 -0400
parents ec202446408a
children de803005027f
comparison
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1:ec202446408a 2:9fbf29a8c12b
1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.4"> 1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6">
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>
7 <version_command interpreter="python">align_back_trans.py --version</version_command>
8 <command interpreter="python">
9 align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
10 </command>
11 <stdio> 7 <stdio>
12 <!-- Anything other than zero is an error --> 8 <!-- Anything other than zero is an error -->
13 <exit_code range="1:" /> 9 <exit_code range="1:" />
14 <exit_code range=":-1" /> 10 <exit_code range=":-1" />
15 </stdio> 11 </stdio>
12 <version_command interpreter="python">align_back_trans.py --version</version_command>
13 <command interpreter="python">
14 align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
15 </command>
16 <inputs> 16 <inputs>
17 <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." /> 17 <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
18 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> 18 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
19 <option value="1">1. Standard</option> 19 <option value="1">1. Standard</option>
20 <option value="2">2. Vertebrate Mitochondrial</option> 20 <option value="2">2. Vertebrate Mitochondrial</option>
36 <option value="0">Don't check the translation</option> 36 <option value="0">Don't check the translation</option>
37 </param> 37 </param>
38 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> 38 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="out_nuc_align" format="input" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/> 41 <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test> 44 <test>
45 <param name="prot_align" value="demo_prot_align.fasta" /> 45 <param name="prot_align" value="demo_prot_align.fasta" />
46 <param name="nuc_file" value="demo_nucs.fasta" /> 46 <param name="nuc_file" value="demo_nucs.fasta" />
120 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. 120 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
121 121
122 This tool is available to install into other Galaxy Instances via the Galaxy 122 This tool is available to install into other Galaxy Instances via the Galaxy
123 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans 123 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
124 </help> 124 </help>
125 <citations>
126 <citation type="doi">10.7717/peerj.167</citation>
127 <citation type="doi">10.1093/bioinformatics/btp163</citation>
128 </citations>
125 </tool> 129 </tool>