Mercurial > repos > bgruening > protein_properties
comparison protein_properties.xml @ 0:cd211b8c2e51 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author | bgruening |
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date | Mon, 20 Nov 2017 05:09:21 -0500 |
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1 <tool id="bg_protein_properties" name="Calculate protein properties" version="0.1.0"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="1.65">biopython</requirement> | |
5 </requirements> | |
6 <command detect_errors="aggressive"><![CDATA[ | |
7 '$__tool_directory__/protein_properties.py' < '$input' > '$output' | |
8 ]]></command> | |
9 <inputs> | |
10 <param format="fasta" name="input" type="data" label="Protein sequence" | |
11 help="This should be in FASTA format." /> | |
12 </inputs> | |
13 <outputs> | |
14 <data format="tabular" name="output" /> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="input" value="Q9LHB9.fasta" ftype="fasta"/> | |
19 <output name="output" file="protein_properties_result1.tabular" ftype="tabular"/> | |
20 </test> | |
21 </tests> | |
22 <help><![CDATA[ | |
23 | |
24 **What it does** | |
25 | |
26 This tool will calculate several properties for each given input sequence. The result will contain the following columns: | |
27 | |
28 - ID of the sequence | |
29 - Molecular weight | |
30 - Isoelectric point | |
31 - *gravy* according to Kyte and Doolittle | |
32 - Length of the sequence | |
33 - Instability index, according to Guruprasad, 1990. (Any value above 40 means the protein is unstable (has a short half life)) | |
34 - Aromaticity, according to Lobry, 1994. (It is simply the relative frequency of Phe+Trp+Tyr) | |
35 - Sequence (as given in the input) | |
36 | |
37 For more information see the `BioPython ProteinAnalysis documentation <http://www.biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html>`_. | |
38 | |
39 ]]></help> | |
40 <citations> | |
41 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
42 </citations> | |
43 </tool> |