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annotate fetch_fasta_from_NCBI.xml @ 1:7e41bbb94159 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
author artbio
date Sun, 15 Oct 2017 13:56:26 -0400
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7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
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1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.1.0">
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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 $dbname
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7 -o '$outfilename'
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8 -l '$logfile'
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9 #if $date_condition.date_filter == "YES":
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10 --datetype $date_condition.datetype
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11 --mindate $date_condition.mindate
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12 --maxdate $date_condition.maxdate
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13 #end if
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14 ]]></command>
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15
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16 <inputs>
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17 <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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18 <sanitizer>
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19 <valid initial="string.printable">
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20 <remove value="&quot;"/>
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21 <remove value="\"/>
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22 </valid>
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23 <mapping initial="none">
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24 <add source="&quot;" target="\&quot;"/>
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25 <add source="\" target="\\"/>
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26 </mapping>
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27 </sanitizer>
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28 </param>
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29 <param name="dbname" type="select" label="NCBI database">
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30 <option value="nuccore">Nucleotide</option>
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31 <option value="protein">Protein</option>
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32 </param>
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33 <conditional name="date_condition">
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34 <param name="date_filter" type="boolean" label="Filter the sequences by date?" truevalue="YES" falsevalue="NO" checked="false"/>
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35 <when value="YES">
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36 <param name="datetype" type="select">
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37 <option value="pdat">Publication date</option>
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38 <option value="mdat">Modification date</option>
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39 </param>
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40 <param name="mindate" type="text" help="Date must follow one of the following formats: YYYY/MM/DD, YYYY/MM or YYYY"/>
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41 <param name="maxdate" type="text" help="Date must follow one of the following formats: YYYY/MM/DD, YYYY/MM or YYYY"/>
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42 </when>
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43 <when value="NO"/>
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44 </conditional>
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45 </inputs>
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46 <outputs>
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47 <data name="outfilename" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" />
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48 <data format="txt" name="logfile" label="${tool.name}: log"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="queryString" value="9629650[gi]" />
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53 <param name="dbname" value="nuccore" />
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54 <output name="outfilename" ftype="fasta" file="output.fa" />
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55 <!-- <output name="logfile" ftype="txt" file="log.txt" /> log.txt changes with timestamp. removed to pass the test -->
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56 </test>
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57 <test>
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58 <param name="queryString" value="CU929326[Accession]" />
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59 <param name="dbname" value="nuccore" />
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60 <param name="date_filter" value="YES"/>
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61 <param name="datetype" value="pdat"/>
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62 <param name="mindate" value="2008/09"/>
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63 <param name="maxdate" value="2008/09"/>
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64 <output name="outfilename" ftype="fasta" file="zebra_output.fa" />
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65 </test>
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66 </tests>
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67 <help>
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68 **What it does**
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69
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70 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query.
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71
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72 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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73
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74 See `Entrez help`_ for explanation of query formats
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75
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76 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
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77
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78 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
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79
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80 **Acknowledgments**
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81
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82 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
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83
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84 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
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85
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86 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
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87 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
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88 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
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89 .. _MIT license: http://opensource.org/licenses/MIT
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90
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91 </help>
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92 <citations>
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93 <citation type="doi">10.1186/1471-2105-14-73</citation>
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94 </citations>
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95 </tool>