Mercurial > repos > iuc > ncbi_eutils_elink

comparison elink.xml @ 3:55b3067762f9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:50:37 +0000
parents 1ed9a99b9b1f
children 9b628ed09553
comparison
equal deleted inserted replaced
2:1ed9a99b9b1f 3:55b3067762f9
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <version_command>python elink.py --version</version_command> 8 <version_command>python elink.py --version</version_command>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 python '$__tool_directory__/elink.py' 10 python '$__tool_directory__/elink.py'
11 #if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'): 11
12 $cmd.db_select_to 12 @LINK_TOKEN@
13 #else:
14 "none"
15 #end if
16
17 $db_select_from
18 $cmd.cmd_select
19 13
20 @EMAIL_ARGUMENTS@ 14 @EMAIL_ARGUMENTS@
21 15
22 @LIST_OR_HIST@ 16 @LIST_OR_HIST@
23
24 #if $cmd.cmd_select == "neighbor_history":
25 --history_out $history
26 #end if
27 17
28 > $default]]></command> 18 > $default]]></command>
29 <inputs> 19 <inputs>
30 <expand macro="dbselect" name="db_select_from" label="From NCBI Database" />
31 <conditional name="cmd">
32 <param name="cmd_select" type="select" label="ELink command to execute">
33 <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option>
34 <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>
35 <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>
36 <option value="acheck">ACheck: List all links available from a set of UIDs</option>
37 <option value="ncheck">NCheck: Check for the existence of links within the same database for a set of UIDs</option>
38 <option value="lcheck">LCheck: Check for the existence of external links (LinkOuts) for a set of UIDs</option>
39 <option value="llinks">Links: For each input UID, list the URLs and attributes for the LinkOut providers that are not libraries</option>
40 <option value="llinkslib">LinksLib: For each input UID, list the URLs and attributes for the LinkOut providers (including libraries)</option>
41 <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option>
42 </param>
43 <when value="neighbor">
44 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
45 </when>
46 <when value="neighbor_score">
47 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
48 </when>
49 <when value="neighbor_history">
50 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
51 </when>
52 <when value="acheck">
53 <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
54 </when>
55 <when value="ncheck"/>
56 <when value="lcheck"/>
57 <when value="llinks"/>
58 <when value="llinkslib"/>
59 <when value="prlinks"/>
60 </conditional>
61 <expand macro="list_or_hist"/> 20 <expand macro="list_or_hist"/>
21 <expand macro="linkmacro"/>
62 </inputs> 22 </inputs>
63 <outputs> 23 <outputs>
64 <data format="xml" name="default" label="NCBI Linked IDs from $db_select_from"/> 24 <data format="xml" name="default" label="NCBI ${cmd.cmd_select} Links From ${cmd.db_from_link.db_select_from_link} To ${cmd.db_from_link.db_to.db_select_to} Via ${cmd.db_from_link.db_to.linkname}">
65 <expand macro="history_out"> 25 <change_format>
66 <filter>cmd['cmd_select'] == 'neighbor_history'</filter> 26 <when input="cmd.output_format" value="xml" format="xml" />
67 </expand> 27 <when input="cmd.output_format" value="json" format="json" />
28 <when input="cmd.output_format" value="text" format="tabular" />
29 </change_format>
30 <filter>query_source['qss'] != 'history_json' and query_source['qss'] != 'history_xml'</filter>
31 </data>
32 <collection name="linksets" type="list" label="NCBI ${cmd.cmd_select} Links From ${cmd.db_from_link.db_select_from_link} To ${cmd.db_from_link.db_to.db_select_to} Via All">
33 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
34 <filter>query_source['qss'] == 'history_json' or query_source['qss'] == 'history_xml'</filter>
35 </collection>
68 </outputs> 36 </outputs>
69 <tests> 37 <tests>
70 <test> 38 <test>
71 <param name="cmd_select" value="neighbor"/> 39 <param name="cmd_select" value="neighbor"/>
72 <param name="db_select_to" value="pubmed"/> 40 <param name="db_select_to" value="pubmed"/>
73 <param name="db_select_from" value="taxonomy"/> 41 <param name="db_select_from_link" value="taxonomy"/>
74 <param name="qss" value="id_list"/> 42 <param name="qss" value="id_list"/>
75 <param name="id_list" value="510899"/> 43 <param name="id_list" value="510899"/>
44 <param name="output_format" value="xml"/>
45 <param name="linkname" value="None"/>
76 <output name="default" file="pm-tax-neighbor.xml" ftype="xml"/> 46 <output name="default" file="pm-tax-neighbor.xml" ftype="xml"/>
47 </test>
48 <test>
49 <param name="cmd_select" value="neighbor"/>
50 <param name="db_select_to" value="nuccore"/>
51 <param name="db_select_from_link" value="gene"/>
52 <param name="qss" value="id_xml"/>
53 <param name="id_xml" value="elink.esearch_in_xmlid.xml"/>
54 <param name="output_format" value="text"/>
55 <param name="linkname" value="gene_nuccore"/>
56 <output name="default" file="elink.esearch_in_xmlid_1link.tabular" ftype="tabular"/>
57 </test>
58 <test>
59 <param name="cmd_select" value="neighbor"/>
60 <param name="db_select_to" value="nuccore"/>
61 <param name="db_select_from_link" value="gene"/>
62 <param name="qss" value="id_json"/>
63 <param name="id_json" value="elink.esearchin_id.json"/>
64 <param name="output_format" value="json"/>
65 <param name="linkname" value="None"/>
66 <output name="default" file="elink.esearchin_id_alllinks.json" ftype="json"/>
67 </test>
68 <test>
69 <param name="cmd_select" value="neighbor"/>
70 <param name="db_select_to" value="nuccore"/>
71 <param name="db_select_from_link" value="gene"/>
72 <param name="qss" value="id_file"/>
73 <param name="id_file" value="elink.esearchin_id.tabular"/>
74 <param name="output_format" value="xml"/>
75 <param name="linkname" value="gene_nuccore_refseqrna"/>
76 <output name="default" file="elink.esearchin_id_1link.xml" ftype="xml"/>
77 </test>
78 <test>
79 <param name="cmd_select" value="neighbor_history"/>
80 <param name="db_select_to" value="gene"/>
81 <param name="db_select_from_link" value="nuccore"/>
82 <param name="qss" value="id_json"/>
83 <param name="id_json" value="elink.elinkin_1link.json"/>
84 <param name="output_format" value="json"/>
85 <param name="linkname" value="nuccore_gene"/>
86 <output name="default" file="elink.elinkin_1link_hist.json" ftype="json" lines_diff="2"/>
87 </test>
88 <test>
89 <param name="cmd_select" value="neighbor_history"/>
90 <param name="db_select_to" value="gene"/>
91 <param name="db_select_from_link" value="nuccore"/>
92 <param name="qss" value="id_xml"/>
93 <param name="id_xml" value="elink.elinkin_alllinks_id.xml"/>
94 <param name="output_format" value="xml"/>
95 <param name="linkname" value="nuccore_gene"/>
96 <output name="default" file="elink.elinkin_allalllinks_id.xml" ftype="xml" lines_diff="2"/>
97 </test>
98 <test>
99 <param name="cmd_select" value="neighbor_score"/>
100 <param name="db_select_to" value="gene"/>
101 <param name="db_select_from_link" value="nuccore"/>
102 <param name="qss" value="id_list"/>
103 <param name="id_list" value="1899688395"/>
104 <param name="output_format" value="text"/>
105 <param name="linkname" value="nuccore_gene"/>
106 <output name="default" file="elink.elinkin_1link_id.tabular" ftype="tabular"/>
77 </test> 107 </test>
78 </tests> 108 </tests>
79 <help><![CDATA[ 109 <help><![CDATA[
80 NCBI Entrez ELink 110 NCBI Entrez ELink
81 ================= 111 =================