Mercurial > repos > iuc > ncbi_entrez_direct_einfo

comparison einfo.xml @ 0:c66f2400ecf8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
author iuc
date Tue, 22 Mar 2022 22:30:36 +0000
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children df0df73c8bda
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-1:000000000000 0:c66f2400ecf8
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>