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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi commit 1a90ac7cdeb35399011207ab43c78043fd5c7287
author artbio
date Sat, 14 Oct 2023 22:34:56 +0000
parents 706fe8139955
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1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="3.0.0"> 1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="3.1.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.25.9">urllib3</requirement> 4 <requirement type="package" version="1.25.9">urllib3</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
62 <filter>query['option'] == "query"</filter> 62 <filter>query['option'] == "query"</filter>
63 </data> 63 </data>
64 <data format="txt" name="logfile" label="logs"/> 64 <data format="txt" name="logfile" label="logs"/>
65 </outputs> 65 </outputs>
66 <tests> 66 <tests>
67 <test> 67 <test expect_num_outputs="3">
68 <param name="queryString" value="9629650[gi]" /> 68 <param name="queryString" value="9629650[gi]" />
69 <param name="dbname" value="nuccore" /> 69 <param name="dbname" value="nuccore" />
70 <param name="fetch_option" value="fasta"/> 70 <param name="fetch_option" value="fasta"/>
71 <output name="fasta" ftype="fasta" file="output.fa" /> 71 <output name="fasta" ftype="fasta" file="output.fa" />
72 </test> 72 </test>
73 <test> 73 <test expect_num_outputs="2">
74 <param name="queryString" value="CU929326[Accession]" /> 74 <param name="queryString" value="CU929326[Accession]" />
75 <param name="dbname" value="nuccore" /> 75 <param name="dbname" value="nuccore" />
76 <param name="fetch_option" value="justiuds"/> 76 <param name="fetch_option" value="justiuds"/>
77 <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/> 77 <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/>
78 </test> 78 </test>
79 <test> 79 <test expect_num_outputs="2">
80 <param name="option" value="list" /> 80 <param name="option" value="list" />
81 <param name="iud_list" value="input_list.txt" ftype="txt" /> 81 <param name="iud_list" value="input_list.txt" ftype="txt" />
82 <param name="dbname" value="nuccore" /> 82 <param name="dbname" value="nuccore" />
83 <param name="fetch_option" value="fasta"/> 83 <param name="fetch_option" value="fasta"/>
84 <output name="fasta" ftype="fasta" file="output_list.fa"/> 84 <output name="fasta" ftype="fasta" file="output_list.fa"/>
85 </test> 85 </test>
86 <test> 86 <test expect_num_outputs="3">
87 <param name="queryString" value="Drosophila[Organism] AND 2017[Modification Date] AND virus" /> 87 <param name="queryString" value="Drosophila[Organism] AND 2017[Modification Date] AND virus" />
88 <param name="dbname" value="nuccore" /> 88 <param name="dbname" value="nuccore" />
89 <param name="fetch_option" value="fasta"/> 89 <param name="fetch_option" value="fasta"/>
90 <output name="fasta" ftype="fasta" > 90 <output name="fasta" ftype="fasta" >
91 <metadata name="sequences" value="9" /> 91 <metadata name="sequences" value="2" />
92 </output> 92 </output>
93 </test> 93 </test>
94 <test> 94 <test expect_num_outputs="2">
95 <param name="queryString" value="labalbalbalbaalablalbabal[Title]" /> 95 <param name="queryString" value="labalbalbalbaalablalbabal[Title]" />
96 <param name="dbname" value="nuccore" /> 96 <param name="dbname" value="nuccore" />
97 <param name="fetch_option" value="justiuds"/> 97 <param name="fetch_option" value="justiuds"/>
98 <output name="logfile" ftype="txt"> 98 <output name="logfile" ftype="txt">
99 <assert_contents> 99 <assert_contents>
103 </test> 103 </test>
104 </tests> 104 </tests>
105 <help> 105 <help>
106 **What it does** 106 **What it does**
107 107
108 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database (nuccore or protein) for a given entrez query. 108 This tool retrieves nucleotide/peptide sequences from the corresponding
109 NCBI database (nuccore or protein) for a given entrez query.
109 110
110 The tool can be set with the query "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose 111 The tool can be set with the query
112 "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]"
113 for metaVisitor use purpose
111 114
112 See `Entrez help`_ for explanation of query formats 115 See `Entrez help`_ for explanation of query formats
113 116
114 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields. 117 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
115 118
116 By checking the checkbox you can also run your query without sequence retrieval and get the number of sequences your query will fetch. 119 By checking the checkbox you can also run your query without sequence
120 retrieval and get the number of sequences your query will fetch.
117 121
118 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset) 122 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
119 123
120 Retrieval progress is reported in the log dataset. 124 Retrieval progress is reported in the log dataset.
121 125
144 log file (default=stderr) 148 log file (default=stderr)
145 --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL} 149 --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
146 logging level (default: INFO) 150 logging level (default: INFO)
147 ]]> 151 ]]>
148 152
149 **Acknowledgments**
150
151 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
152
153 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
154 153
155 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options 154 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
156 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
157 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
158 .. _MIT license: http://opensource.org/licenses/MIT
159 155
160 </help> 156 </help>
161 <citations> 157 <citations>
162 <citation type="doi">10.1186/1471-2105-14-73</citation> 158 <citation type="doi">10.1186/1471-2105-14-73</citation>
163 </citations> 159 </citations>