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comparison tools/align_back_trans/align_back_trans.xml @ 4:c8469274d136 draft

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v0.0.8 Using Biopython 1.67 from Tool Shed or Conda package
author peterjc
date Wed, 10 May 2017 12:05:28 -0400
parents de803005027f
children 2c32e8a8990f
comparison
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3:de803005027f 4:c8469274d136
1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.7"> 1 <tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.8">
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="1.67">biopython</requirement>
5 <requirement type="python-module">Bio</requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <version_command>
8 <!-- Anything other than zero is an error --> 7 python $__tool_directory__/align_back_trans.py --version
9 <exit_code range="1:" /> 8 </version_command>
10 <exit_code range=":-1" /> 9 <command detect_errors="aggressive">
11 </stdio> 10 python $__tool_directory__/align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table'
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> 11 </command>
16 <inputs> 12 <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." /> 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." />
18 <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">
19 <option value="1">1. Standard</option> 15 <option value="1">1. Standard</option>
31 <option value="15">15. Blepharisma Macronuclear</option> 27 <option value="15">15. Blepharisma Macronuclear</option>
32 <option value="16">16. Chlorophycean Mitochondrial</option> 28 <option value="16">16. Chlorophycean Mitochondrial</option>
33 <option value="21">21. Trematode Mitochondrial</option> 29 <option value="21">21. Trematode Mitochondrial</option>
34 <option value="22">22. Scenedesmus obliquus</option> 30 <option value="22">22. Scenedesmus obliquus</option>
35 <option value="23">23. Thraustochytrium Mitochondrial</option> 31 <option value="23">23. Thraustochytrium Mitochondrial</option>
32 <option value="24">24. Pterobranchia Mitochondrial</option>
33 <option value="25">25. Candidate Division SR1 and Gracilibacteria</option>
34 <!-- TODO, these are not in Biopython 1.67
35 <option value="26">26. Pachysolen tannophilus Nuclear</option>
36 <option value="26">27. Karyorelict Nuclear</option>
37 <option value="26">28. Condylostoma Nuclear</option>
38 <option value="26">29. Mesodinium Nuclear</option>
39 <option value="26">30. Peritrich Nuclear</option>
40 <option value="26">31. Blastocrithidia Nuclear</option>
41 -->
36 <option value="0">Don't check the translation</option> 42 <option value="0">Don't check the translation</option>
37 </param> 43 </param>
38 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> 44 <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
39 </inputs> 45 </inputs>
40 <outputs> 46 <outputs>