Mercurial > repos > iuc > ncbi_entrez_direct_einfo
comparison einfo.xml @ 0:c66f2400ecf8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
author | iuc |
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date | Tue, 22 Mar 2022 22:30:36 +0000 |
parents | |
children | df0df73c8bda |
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1 <tool id="ncbi_entrez_direct_einfo" name="NCBI EInfo" version="@TOOL_VERSION@"> | |
2 <description>fetch NCBI database metadata</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <version_command>einfo -version</version_command> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 @ECONTACT@ | |
10 einfo | |
11 #if str( $db.target ) == "dbs": | |
12 -dbs | |
13 #else: | |
14 -db "${db.db}" | |
15 #end if | |
16 > '${output_xml}' | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <conditional name="db"> | |
21 <param name="target" type="select" label="List DBs or Info on a DB"> | |
22 <option value="db" selected="True">DB info</option> | |
23 <option value="dbs">List of DBs</option> | |
24 </param> | |
25 <when value="dbs"/> | |
26 <when value="db"> | |
27 <param name="db" type="select" label="Choose your DB" argument="-db"> | |
28 <option value="annotinfo">annotinfo</option> | |
29 <option value="assembly">assembly</option> | |
30 <option value="bioproject">bioproject</option> | |
31 <option value="biosample">biosample</option> | |
32 <option value="biosystems">biosystems</option> | |
33 <option value="blastdbinfo">blastdbinfo</option> | |
34 <option value="books">books</option> | |
35 <option value="cdd">cdd</option> | |
36 <option value="clinvar">clinvar</option> | |
37 <option value="clone">clone</option> | |
38 <option value="dbvar">dbvar</option> | |
39 <option value="gap">gap</option> | |
40 <option value="gapplus">gapplus</option> | |
41 <option value="gds">gds</option> | |
42 <option value="gencoll">gencoll</option> | |
43 <option value="gene">gene</option> | |
44 <option value="genome">genome</option> | |
45 <option value="geoprofiles">geoprofiles</option> | |
46 <option value="grasp">grasp</option> | |
47 <option value="gtr">gtr</option> | |
48 <option value="homologene">homologene</option> | |
49 <option value="medgen">medgen</option> | |
50 <option value="mesh">mesh</option> | |
51 <option value="ncbisearch">ncbisearch</option> | |
52 <option value="nlmcatalog">nlmcatalog</option> | |
53 <option value="nuccore">nuccore</option> | |
54 <option value="nucest">nucest</option> | |
55 <option value="nucgss">nucgss</option> | |
56 <option value="nucleotide">nucleotide</option> | |
57 <option value="omim">omim</option> | |
58 <option value="orgtrack">orgtrack</option> | |
59 <option value="pcassay">pcassay</option> | |
60 <option value="pccompound">pccompound</option> | |
61 <option value="pcsubstance">pcsubstance</option> | |
62 <option value="pmc">pmc</option> | |
63 <option value="popset">popset</option> | |
64 <option value="probe">probe</option> | |
65 <option value="protein">protein</option> | |
66 <option value="proteinclusters">proteinclusters</option> | |
67 <option value="pubmed">pubmed</option> | |
68 <option value="pubmedhealth">pubmedhealth</option> | |
69 <option value="seqannot">seqannot</option> | |
70 <option value="snp">snp</option> | |
71 <option value="sra">sra</option> | |
72 <option value="structure">structure</option> | |
73 <option value="taxonomy">taxonomy</option> | |
74 <option value="unigene">unigene</option> | |
75 </param> | |
76 </when> | |
77 </conditional> | |
78 </inputs> | |
79 <outputs> | |
80 <data format="xml" name="output_xml"/> | |
81 </outputs> | |
82 <tests> | |
83 <test> | |
84 <param name="db|target" value="db"/> | |
85 <param name="db|db" value="sra"/> | |
86 <output name="output_xml"> | |
87 <assert_contents> | |
88 <has_text_matching expression="SRA" /> | |
89 </assert_contents> | |
90 </output> | |
91 </test> | |
92 </tests> | |
93 <help><![CDATA[ | |
94 NCBI Entrez EInfo | |
95 ================= | |
96 | |
97 Provides the number of records indexed in each field of a given database, the | |
98 date of the last update of the database, and the available links from the | |
99 database to other Entrez databases. | |
100 | |
101 @DISCLAIMER@ | |
102 ]]></help> | |
103 <expand macro="citations"/> | |
104 </tool> |