Mercurial > repos > artbio > fetch_fasta_from_ncbi

annotate fetch_fasta_from_NCBI.xml @ 3:8be88084f89c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
author artbio
date Wed, 08 Nov 2017 13:00:26 -0500
parents 50f5ef3313bb
children c667d0ee39f5
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8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
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1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.2.1">
1
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2 <description></description>
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3 <command><![CDATA[
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4 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
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5 -i "$queryString"
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6 -d $dbname
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7 -l '$logfile'
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8 $dry_run
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9 -o '$outfile'
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10 ]]></command>
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12 <inputs>
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13 <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]">
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14 <sanitizer>
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15 <valid initial="string.printable">
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16 <remove value="&quot;"/>
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17 <remove value="\"/>
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18 </valid>
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19 <mapping initial="none">
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20 <add source="&quot;" target="\&quot;"/>
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21 <add source="\" target="\\"/>
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22 </mapping>
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23 </sanitizer>
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24 </param>
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25 <param name="dbname" type="select" label="NCBI database">
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26 <option value="nuccore">Nucleotide</option>
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27 <option value="protein">Protein</option>
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28 </param>
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29 <param name="dry_run" type="boolean" label="Dry run to get the number of sequences?" truevalue="--count" falsevalue="" checked="false"/>
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30 </inputs>
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31 <outputs>
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32 <data name="outfile" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" >
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33 <filter> dry_run == False</filter>
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34 </data>
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35 <data format="txt" name="logfile" label="${tool.name}: log"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="queryString" value="9629650[gi]" />
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40 <param name="dbname" value="nuccore" />
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41 <output name="outfilename" ftype="fasta" file="output.fa" />
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42 </test>
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43 <test>
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44 <param name="queryString" value="CU929326[Accession]" />
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45 <param name="dbname" value="nuccore" />
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46 <param name="date_filter" value="1"/>
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47 <param name="dry_run" value="True"/>
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48 <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/>
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49 </test>
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50 </tests>
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51 <help>
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52 **What it does**
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54 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query.
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56 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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58 See `Entrez help`_ for explanation of query formats
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60 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
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62 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
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64 **Acknowledgments**
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66 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
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68 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
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70 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
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71 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
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72 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
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73 .. _MIT license: http://opensource.org/licenses/MIT
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75 </help>
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76 <citations>
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77 <citation type="doi">10.1186/1471-2105-14-73</citation>
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78 </citations>
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79 </tool>