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1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.2">
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2 <description></description>
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3 <command interpreter="python">retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile </command>
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4
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5 <inputs>
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6 <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]">
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7 <sanitizer>
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8 <valid initial="string.printable">
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9 <remove value="""/>
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10 <remove value="\"/>
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11 </valid>
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12 <mapping initial="none">
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13 <add source=""" target="\""/>
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14 <add source="\" target="\\"/>
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15 </mapping>
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16 </sanitizer>
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17 </param>
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18 <param name="dbname" type="select" label="NCBI database">
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19 <option value="nuccore">Nucleotide</option>
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20 <option value="protein">Protein</option>
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21 <!-- <option value="pubmed">Pubmed (experimental)</option> -->
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: queryString${queryString.value}.${dbname.value_label}.fasta" />
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26 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="queryString" value="DCV AND virus" />
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31 <param name="dbname" value="nuccore" />
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32 <output name="outfilename" ftype="fasta" file="output.fa" />
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33 <!-- <output name="logfile" ftype="txt" file="log.txt" /> log.txt changes with timestamp. removed to pass the test -->
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34 </test>
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35 </tests>
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36 <help>
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37 **What it does**
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38
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39 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query.
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40
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41 The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose
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42
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43 See `Entrez help`_ for explanation of query formats
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44
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45 **Acknowledgments**
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46
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47 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
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48
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49 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
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50
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51 .. _Entrez help: http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
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52 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
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53 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
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54 .. _MIT license: http://opensource.org/licenses/MIT
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55
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56 </help>
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57 </tool>
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