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comparison elink.xml @ 0:59063d2e91c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:40:20 -0400
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children 1ed9a99b9b1f
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-1:000000000000 0:59063d2e91c6
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 <version_command>python elink.py --version</version_command>
9 <command detect_errors="aggressive" interpreter="python"><![CDATA[elink.py
10 #if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'):
11 $cmd.db_select_to
12 #else:
13 "none"
14 #end if
15
16 $db_select_from
17 $cmd.cmd_select
18
19 @EMAIL_ARGUMENTS@
20
21 @LIST_OR_HIST@
22
23 #if $cmd.cmd_select == "neighbor_history":
24 --history_out $history
25 #end if
26
27 > $default]]></command>
28 <inputs>
29 <expand macro="dbselect" name="db_select_from" label="From NCBI Database" />
30 <conditional name="cmd">
31 <param name="cmd_select" type="select" label="ELink command to execute">
32 <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option>
33 <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>
34 <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>
35 <option value="acheck">ACheck: List all links available from a set of UIDs</option>
36 <option value="ncheck">NCheck: Check for the existence of links within the same database for a set of UIDs</option>
37 <option value="lcheck">LCheck: Check for the existence of external links (LinkOuts) for a set of UIDs</option>
38 <option value="llinks">Links: For each input UID, list the URLs and attributes for the LinkOut providers that are not libraries</option>
39 <option value="llinkslib">LinksLib: For each input UID, list the URLs and attributes for the LinkOut providers (including libraries)</option>
40 <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option>
41 </param>
42 <when value="neighbor">
43 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
44 </when>
45 <when value="neighbor_score">
46 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
47 </when>
48 <when value="neighbor_history">
49 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
50 </when>
51 <when value="acheck">
52 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
53 </when>
54 <when value="ncheck"/>
55 <when value="lcheck"/>
56 <when value="llinks"/>
57 <when value="llinkslib"/>
58 <when value="prlinks"/>
59 </conditional>
60 <expand macro="list_or_hist"/>
61 </inputs>
62 <outputs>
63 <data format="xml" name="default" label="NCBI Linked IDs from $db_select_from"/>
64 <expand macro="history_out">
65 <filter>cmd['cmd_select'] == 'neighbor_history'</filter>
66 </expand>
67 </outputs>
68 <tests>
69 <test>
70 <param name="cmd_select" value="neighbor"/>
71 <param name="db_select_to" value="pubmed"/>
72 <param name="db_select_from" value="taxonomy"/>
73 <param name="qss" value="id_list"/>
74 <param name="id_list" value="510899"/>
75 <output name="default" file="pm-tax-neighbor.xml" ftype="xml"/>
76 </test>
77 </tests>
78 <help><![CDATA[
79 NCBI Entrez ELink
80 =================
81
82 Responds to a list of UIDs in a given database with either a list of related
83 UIDs (and relevancy scores) in the same database or a list of linked UIDs in
84 another Entrez database; checks for the existence of a specified link from a
85 list of one or more UIDs; creates a hyperlink to the primary LinkOut provider
86 for a specific UID and database, or lists LinkOut URLs and attributes for
87 multiple UIDs.
88
89 Commands
90 --------
91
92 Example Queries
93 ---------------
94
95 Link from protein to gene
96
97 +----------------------+--------------------------------------+
98 | Parameter | Value |
99 +======================+======================================+
100 | From NCBI Database | Protein |
101 +----------------------+--------------------------------------+
102 | Elink Command | Neighbor |
103 +----------------------+--------------------------------------+
104 | To NCBI Database | Gene |
105 +----------------------+--------------------------------------+
106 | ID List | 15718680 157427902 |
107 +----------------------+--------------------------------------+
108
109 Find related articles to PMID 20210808 with scores
110
111 +----------------------+--------------------------------------+
112 | Parameter | Value |
113 +======================+======================================+
114 | From NCBI Database | PubMed |
115 +----------------------+--------------------------------------+
116 | Elink Command | Scored Neighbors |
117 +----------------------+--------------------------------------+
118 | To NCBI Database | PubMed |
119 +----------------------+--------------------------------------+
120 | ID List | 20210808 |
121 +----------------------+--------------------------------------+
122
123 List all possible links from two protein GIs
124
125 +----------------------+--------------------------------------+
126 | Parameter | Value |
127 +======================+======================================+
128 | From NCBI Database | Protein |
129 +----------------------+--------------------------------------+
130 | Elink Command | ACheck |
131 +----------------------+--------------------------------------+
132 | ID List | 15718680 157427902 |
133 +----------------------+--------------------------------------+
134
135 List all possible links from two protein GIs to PubMed
136
137 +----------------------+--------------------------------------+
138 | Parameter | Value |
139 +======================+======================================+
140 | From NCBI Database | Protein |
141 +----------------------+--------------------------------------+
142 | Elink Command | ACheck |
143 +----------------------+--------------------------------------+
144 | To NCBI Database | PubMed |
145 +----------------------+--------------------------------------+
146 | ID List | 15718680 157427902 |
147 +----------------------+--------------------------------------+
148
149 Check whether two nuccore sequences have "related sequences" links.
150
151 +----------------------+--------------------------------------+
152 | Parameter | Value |
153 +======================+======================================+
154 | From NCBI Database | Nuccore |
155 +----------------------+--------------------------------------+
156 | Elink Command | NCheck |
157 +----------------------+--------------------------------------+
158 | ID List | 21614549 219152114 |
159 +----------------------+--------------------------------------+
160
161 List the LinkOut URLs for non-library providers for two pubmed abstracts.
162
163 +----------------------+--------------------------------------+
164 | Parameter | Value |
165 +======================+======================================+
166 | From NCBI Database | Pubmed |
167 +----------------------+--------------------------------------+
168 | Elink Command | Links |
169 +----------------------+--------------------------------------+
170 | ID List | 19880848 19822630 |
171 +----------------------+--------------------------------------+
172
173 Find links to full text providers for two PubMed abstracts.
174
175 +----------------------+--------------------------------------+
176 | Parameter | Value |
177 +======================+======================================+
178 | From NCBI Database | Pubmed |
179 +----------------------+--------------------------------------+
180 | Elink Command | Provider Links |
181 +----------------------+--------------------------------------+
182 | ID List | 19880848 19822630 |
183 +----------------------+--------------------------------------+
184
185 @REFERENCES@
186
187 @DISCLAIMER@
188 ]]></help>
189 <expand macro="citations"/>
190 </tool>