fetch_fasta_from_ncbi: retrieve_fasta_from

annotate retrieve_fasta_from_NCBI.xml @ 13:639daa4c3c1a draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca132a4b5d5d7175e6e8bd62cc518397d14dad17

author	drosofff
date	Mon, 15 May 2017 03:10:35 -0400
parents	0bec3cba5c56
children	54941746784b

rev	line source
13 639daa4c3c1a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca132a4b5d5d7175e6e8bd62cc518397d14dad17 drosofff parents: 12 diff changeset	1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="1.0.0">
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	2 <description></description>
12 0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	3 <command><![CDATA[
0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	4 python '$__tool_directory__'/retrieve_fasta_from_NCBI.py
0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	5 -i "$queryString"
0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	6 -d $dbname
0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	7 -o '$outfilename'
0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	8 -l '$logfile'
0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	9 ]]></command>
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	10
4b34f2b5c14e Uploaded drosofff parents: diff changeset	11 <inputs>
6 fe9549854fa2 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 4 diff changeset	12 <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 4b34f2b5c14e Uploaded drosofff parents: diff changeset	13 <sanitizer>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	14 <valid initial="string.printable">
4b34f2b5c14e Uploaded drosofff parents: diff changeset	15 <remove value="""/>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	16 <remove value="\"/>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	17 </valid>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	18 <mapping initial="none">
4b34f2b5c14e Uploaded drosofff parents: diff changeset	19 <add source=""" target="\""/>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	20 <add source="\" target="\\"/>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	21 </mapping>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	22 </sanitizer>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	23 </param>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	24 <param name="dbname" type="select" label="NCBI database">
4b34f2b5c14e Uploaded drosofff parents: diff changeset	25 <option value="nuccore">Nucleotide</option>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	26 <option value="protein">Protein</option>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	27 </param>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	28 </inputs>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	29 <outputs>
11 962054e7c2de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit fae2061eadac000cdb408d0db76226620c8860a6 drosofff parents: 10 diff changeset	30 <data name="outfilename" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" />
962054e7c2de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit fae2061eadac000cdb408d0db76226620c8860a6 drosofff parents: 10 diff changeset	31 <data format="txt" name="logfile" label="${tool.name}: log"/>
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	32 </outputs>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	33 <tests>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	34 <test>
9 f57ebdc7ad56 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 6 diff changeset	35 <param name="queryString" value="9629650[gi]" />
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	36 <param name="dbname" value="nuccore" />
4b34f2b5c14e Uploaded drosofff parents: diff changeset	37 <output name="outfilename" ftype="fasta" file="output.fa" />
4b34f2b5c14e Uploaded drosofff parents: diff changeset	38 <!-- <output name="logfile" ftype="txt" file="log.txt" /> log.txt changes with timestamp. removed to pass the test -->
4b34f2b5c14e Uploaded drosofff parents: diff changeset	39 </test>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	40 </tests>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	41 <help>
4b34f2b5c14e Uploaded drosofff parents: diff changeset	42 What it does
4b34f2b5c14e Uploaded drosofff parents: diff changeset	43
4b34f2b5c14e Uploaded drosofff parents: diff changeset	44 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query.
4b34f2b5c14e Uploaded drosofff parents: diff changeset	45
4b34f2b5c14e Uploaded drosofff parents: diff changeset	46 The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose
4b34f2b5c14e Uploaded drosofff parents: diff changeset	47
4b34f2b5c14e Uploaded drosofff parents: diff changeset	48 See `Entrez help`_ for explanation of query formats
4b34f2b5c14e Uploaded drosofff parents: diff changeset	49
3 c35b4867c884 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	50 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
c35b4867c884 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	51
c35b4867c884 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	52 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
c35b4867c884 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	53
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	54 Acknowledgments
4b34f2b5c14e Uploaded drosofff parents: diff changeset	55
4b34f2b5c14e Uploaded drosofff parents: diff changeset	56 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
4b34f2b5c14e Uploaded drosofff parents: diff changeset	57
4b34f2b5c14e Uploaded drosofff parents: diff changeset	58 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
4b34f2b5c14e Uploaded drosofff parents: diff changeset	59
12 0bec3cba5c56 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 11 diff changeset	60 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	61 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
4b34f2b5c14e Uploaded drosofff parents: diff changeset	62 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
4b34f2b5c14e Uploaded drosofff parents: diff changeset	63 .. _MIT license: http://opensource.org/licenses/MIT
4b34f2b5c14e Uploaded drosofff parents: diff changeset	64
4b34f2b5c14e Uploaded drosofff parents: diff changeset	65 </help>
4 aa61d63b7e31 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 3 diff changeset	66 <citations>
aa61d63b7e31 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 3 diff changeset	67 <citation type="doi">10.1186/1471-2105-14-73</citation>
aa61d63b7e31 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 3 diff changeset	68 </citations>
0 4b34f2b5c14e Uploaded drosofff parents: diff changeset	69 </tool>

Mercurial > repos > drosofff > fetch_fasta_from_ncbi

annotate retrieve_fasta_from_NCBI.xml @ 13:639daa4c3c1a draft