Mercurial > repos > drosofff > fetch_fasta_from_ncbi
annotate retrieve_fasta_from_NCBI.xml @ 10:2c5375809c03 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit e0a1114b735bf1af257456174f64e5ef8d205754-dirty
| author | drosofff |
|---|---|
| date | Wed, 28 Oct 2015 11:24:45 -0400 |
| parents | f57ebdc7ad56 |
| children | 962054e7c2de |
| rev | line source |
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2c5375809c03
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit e0a1114b735bf1af257456174f64e5ef8d205754-dirty
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1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.3"> |
| 0 | 2 <description></description> |
| 3 <command interpreter="python">retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile </command> | |
| 4 | |
| 5 <inputs> | |
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6 <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]"> |
| 0 | 7 <sanitizer> |
| 8 <valid initial="string.printable"> | |
| 9 <remove value="""/> | |
| 10 <remove value="\"/> | |
| 11 </valid> | |
| 12 <mapping initial="none"> | |
| 13 <add source=""" target="\""/> | |
| 14 <add source="\" target="\\"/> | |
| 15 </mapping> | |
| 16 </sanitizer> | |
| 17 </param> | |
| 18 <param name="dbname" type="select" label="NCBI database"> | |
| 19 <option value="nuccore">Nucleotide</option> | |
| 20 <option value="protein">Protein</option> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: queryString${queryString.value}.${dbname.value_label}.fasta" /> | |
| 25 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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29 <param name="queryString" value="9629650[gi]" /> |
| 0 | 30 <param name="dbname" value="nuccore" /> |
| 31 <output name="outfilename" ftype="fasta" file="output.fa" /> | |
| 32 <!-- <output name="logfile" ftype="txt" file="log.txt" /> log.txt changes with timestamp. removed to pass the test --> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help> | |
| 36 **What it does** | |
| 37 | |
| 38 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query. | |
| 39 | |
| 40 The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose | |
| 41 | |
| 42 See `Entrez help`_ for explanation of query formats | |
| 43 | |
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44 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields. |
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45 |
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46 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset) |
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47 |
| 0 | 48 **Acknowledgments** |
| 49 | |
| 50 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_. | |
| 51 | |
| 52 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. | |
| 53 | |
| 54 .. _Entrez help: http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options | |
| 55 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon | |
| 56 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en | |
| 57 .. _MIT license: http://opensource.org/licenses/MIT | |
| 58 | |
| 59 </help> | |
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60 <citations> |
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61 <citation type="doi">10.1186/1471-2105-14-73</citation> |
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62 </citations> |
| 0 | 63 </tool> |