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comparison elink.xml @ 0:ffc6d6234c8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
author iuc
date Sat, 31 Oct 2015 12:44:05 -0400
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children 127515819562
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-1:000000000000 0:ffc6d6234c8a
1 <?xml version="1.0"?>
2 <tool id="ncbi_eutils_elink" name="NCBI ELink" version="@WRAPPER_VERSION@">
3 <description>link UIDs from one database to another</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <version_command>python elink.py --version</version_command>
10 <command interpreter="python"><![CDATA[elink.py
11 #if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'):
12 $cmd.db_select_to
13 #else:
14 "none"
15 #end if
16
17 $db_select_from
18 $cmd.cmd_select
19
20 @EMAIL_ARGUMENTS@
21
22 @LIST_OR_HIST@
23
24 #if $cmd.cmd_select == "neighbor_history":
25 --history_out $history
26 #end if
27
28 > $default]]></command>
29 <inputs>
30 <param name="db_select_from" type="select" label="From NCBI Database">
31 <option value="assembly">Assembly</option>
32 <option value="bioproject">BioProject</option>
33 <option value="biosample">BioSample</option>
34 <option value="biosystems">Biosystems</option>
35 <option value="blastdbinfo">Blast Database Information</option>
36 <option value="books">Books</option>
37 <option value="cdd">Conserved Domains</option>
38 <option value="clinvar">Clinical Variants</option>
39 <option value="clone">CLone</option>
40 <option value="dbvar">dbVar</option>
41 <option value="epigenomics">Epigenomics</option>
42 <option value="gap">dbGaP</option>
43 <option value="gds">GEO Datasets</option>
44 <option value="gene">Gene</option>
45 <option value="genome">Genome</option>
46 <option value="geoprofiles">GEO Profiles</option>
47 <option value="gtr">Genetic Testing Registry</option>
48 <option value="homologene">HomoloGene</option>
49 <option value="journals">Journals</option>
50 <option value="medgen">MedGen</option>
51 <option value="mesh">MeSH</option>
52 <option value="ncbisearch">NCBI Web Site</option>
53 <option value="nlmcatalog">NLM Catalog</option>
54 <option value="nuccore">Nucleotide</option>
55 <option value="nucest">EST</option>
56 <option value="nucgss">GSS</option>
57 <option value="omim">OMIM</option>
58 <option value="pcassay">PubChem BioAssay</option>
59 <option value="pccompound">PubChem Compound</option>
60 <option value="pcsubstance">PubChem Substance</option>
61 <option value="pmc">PubMed Central</option>
62 <option value="popset">PopSet</option>
63 <option value="probe">Probe</option>
64 <option value="protein">Protein</option>
65 <option value="proteinclusters">Protein Clusters</option>
66 <option value="pubmed">PubMed</option>
67 <option value="pubmedhealth">PubMed Health</option>
68 <option value="snp">SNP</option>
69 <option value="sra">SRA</option>
70 <option value="structure">Structure</option>
71 <option value="taxonomy">Taxonomy</option>
72 <option value="toolkit">NCBI C++ Toolkit</option>
73 <option value="toolkitall">NCBI C++ Toolkit All</option>
74 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
75 <option value="unigene">UniGene</option>
76 </param>
77 <conditional name="cmd">
78 <param name="cmd_select" type="select" label="ELink command to execute">
79 <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option>
80 <option value="neighbor_score">Scored Neighbors: Fetch a set of UIDs within the same database as the input UIDs along with computed similarity scores</option>
81 <option value="neighbor_history">Neighbor (history): Fetch a set of UIDs in DB linked to input UIDs from DBFROM, and store on history server</option>
82 <option value="acheck">ACheck: List all links available from a set of UIDs</option>
83 <option value="ncheck">NCheck: Check for the existence of links within the same database for a set of UIDs</option>
84 <option value="lcheck">LCheck: Check for the existence of external links (LinkOuts) for a set of UIDs</option>
85 <option value="llinks">Links: For each input UID, list the URLs and attributes for the LinkOut providers that are not libraries</option>
86 <option value="llinkslib">LinksLib: For each input UID, list the URLs and attributes for the LinkOut providers (including libraries)</option>
87 <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option>
88 </param>
89 <when value="neighbor">
90 <expand macro="db_select_to"/>
91 </when>
92 <when value="neighbor_score">
93 <expand macro="db_select_to"/>
94 </when>
95 <when value="neighbor_history">
96 <expand macro="db_select_to"/>
97 </when>
98 <when value="acheck">
99 <expand macro="db_select_to"/>
100 </when>
101 <when value="ncheck"/>
102 <when value="lcheck"/>
103 <when value="llinks"/>
104 <when value="llinkslib"/>
105 <when value="prlinks"/>
106 </conditional>
107 <expand macro="list_or_hist"/>
108 </inputs>
109 <outputs>
110 <data format="xml" name="default" label="NCBI Linked IDs from $db_select_from"/>
111 <expand macro="history_out">
112 <filter>cmd['cmd_select'] == 'neighbor_history'</filter>
113 </expand>
114 </outputs>
115 <tests>
116 <test>
117 <param name="cmd_select" value="neighbor"/>
118 <param name="db_select_to" value="pubmed"/>
119 <param name="db_select_from" value="taxonomy"/>
120 <param name="qss" value="id_list"/>
121 <param name="id_list" value="510899"/>
122 <output name="default" file="pm-tax-neighbor.xml"/>
123 </test>
124 </tests>
125 <help><![CDATA[
126 NCBI Entrez ELink
127 =================
128
129 Responds to a list of UIDs in a given database with either a list of related
130 UIDs (and relevancy scores) in the same database or a list of linked UIDs in
131 another Entrez database; checks for the existence of a specified link from a
132 list of one or more UIDs; creates a hyperlink to the primary LinkOut provider
133 for a specific UID and database, or lists LinkOut URLs and attributes for
134 multiple UIDs.
135
136 Commands
137 --------
138
139 Example Queries
140 ---------------
141
142 Link from protein to gene
143
144 +----------------------+--------------------------------------+
145 | Parameter | Value |
146 +======================+======================================+
147 | From NCBI Database | Protein |
148 +----------------------+--------------------------------------+
149 | Elink Command | Neighbor |
150 +----------------------+--------------------------------------+
151 | To NCBI Database | Gene |
152 +----------------------+--------------------------------------+
153 | ID List | 15718680 157427902 |
154 +----------------------+--------------------------------------+
155
156 Find related articles to PMID 20210808 with scores
157
158 +----------------------+--------------------------------------+
159 | Parameter | Value |
160 +======================+======================================+
161 | From NCBI Database | PubMed |
162 +----------------------+--------------------------------------+
163 | Elink Command | Scored Neighbors |
164 +----------------------+--------------------------------------+
165 | To NCBI Database | PubMed |
166 +----------------------+--------------------------------------+
167 | ID List | 20210808 |
168 +----------------------+--------------------------------------+
169
170 List all possible links from two protein GIs
171
172 +----------------------+--------------------------------------+
173 | Parameter | Value |
174 +======================+======================================+
175 | From NCBI Database | Protein |
176 +----------------------+--------------------------------------+
177 | Elink Command | ACheck |
178 +----------------------+--------------------------------------+
179 | ID List | 15718680 157427902 |
180 +----------------------+--------------------------------------+
181
182 List all possible links from two protein GIs to PubMed
183
184 +----------------------+--------------------------------------+
185 | Parameter | Value |
186 +======================+======================================+
187 | From NCBI Database | Protein |
188 +----------------------+--------------------------------------+
189 | Elink Command | ACheck |
190 +----------------------+--------------------------------------+
191 | To NCBI Database | PubMed |
192 +----------------------+--------------------------------------+
193 | ID List | 15718680 157427902 |
194 +----------------------+--------------------------------------+
195
196 Check whether two nuccore sequences have "related sequences" links.
197
198 +----------------------+--------------------------------------+
199 | Parameter | Value |
200 +======================+======================================+
201 | From NCBI Database | Nuccore |
202 +----------------------+--------------------------------------+
203 | Elink Command | NCheck |
204 +----------------------+--------------------------------------+
205 | ID List | 21614549 219152114 |
206 +----------------------+--------------------------------------+
207
208 List the LinkOut URLs for non-library providers for two pubmed abstracts.
209
210 +----------------------+--------------------------------------+
211 | Parameter | Value |
212 +======================+======================================+
213 | From NCBI Database | Pubmed |
214 +----------------------+--------------------------------------+
215 | Elink Command | Links |
216 +----------------------+--------------------------------------+
217 | ID List | 19880848 19822630 |
218 +----------------------+--------------------------------------+
219
220 Find links to full text providers for two PubMed abstracts.
221
222 +----------------------+--------------------------------------+
223 | Parameter | Value |
224 +======================+======================================+
225 | From NCBI Database | Pubmed |
226 +----------------------+--------------------------------------+
227 | Elink Command | Provider Links |
228 +----------------------+--------------------------------------+
229 | ID List | 19880848 19822630 |
230 +----------------------+--------------------------------------+
231
232 @REFERENCES@
233
234 @DISCLAIMER@
235 ]]></help>
236 <expand macro="citations"/>
237 </tool>