Mercurial > repos > iuc > ncbi_eutils_elink
diff elink.xml @ 0:59063d2e91c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author | iuc |
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date | Thu, 07 Jul 2016 02:40:20 -0400 |
parents | |
children | 1ed9a99b9b1f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/elink.xml Thu Jul 07 02:40:20 2016 -0400 @@ -0,0 +1,190 @@ +<?xml version="1.0"?> +<tool id="ncbi_eutils_elink" name="NCBI ELink" version="@WRAPPER_VERSION@"> + <description>link UIDs from one database to another</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>python elink.py --version</version_command> + <command detect_errors="aggressive" interpreter="python"><![CDATA[elink.py +#if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'): + $cmd.db_select_to +#else: + "none" +#end if + +$db_select_from +$cmd.cmd_select + +@EMAIL_ARGUMENTS@ + +@LIST_OR_HIST@ + +#if $cmd.cmd_select == "neighbor_history": + --history_out $history +#end if + +> $default]]></command> + <inputs> + <expand macro="dbselect" name="db_select_from" label="From NCBI Database" /> + <conditional name="cmd"> + <param name="cmd_select" type="select" label="ELink command to execute"> + <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option> + <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> + <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> + <option value="acheck">ACheck: List all links available from a set of UIDs</option> + <option value="ncheck">NCheck: Check for the existence of links within the same database for a set of UIDs</option> + <option value="lcheck">LCheck: Check for the existence of external links (LinkOuts) for a set of UIDs</option> + <option value="llinks">Links: For each input UID, list the URLs and attributes for the LinkOut providers that are not libraries</option> + <option value="llinkslib">LinksLib: For each input UID, list the URLs and attributes for the LinkOut providers (including libraries)</option> + <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option> + </param> + <when value="neighbor"> + <expand macro="dbselect" name="db_select_to" label="To NCBI Database" /> + </when> + <when value="neighbor_score"> + <expand macro="dbselect" name="db_select_to" label="To NCBI Database" /> + </when> + <when value="neighbor_history"> + <expand macro="dbselect" name="db_select_to" label="To NCBI Database" /> + </when> + <when value="acheck"> + <expand macro="dbselect" name="db_select_to" label="To NCBI Database" /> + </when> + <when value="ncheck"/> + <when value="lcheck"/> + <when value="llinks"/> + <when value="llinkslib"/> + <when value="prlinks"/> + </conditional> + <expand macro="list_or_hist"/> + </inputs> + <outputs> + <data format="xml" name="default" label="NCBI Linked IDs from $db_select_from"/> + <expand macro="history_out"> + <filter>cmd['cmd_select'] == 'neighbor_history'</filter> + </expand> + </outputs> + <tests> + <test> + <param name="cmd_select" value="neighbor"/> + <param name="db_select_to" value="pubmed"/> + <param name="db_select_from" value="taxonomy"/> + <param name="qss" value="id_list"/> + <param name="id_list" value="510899"/> + <output name="default" file="pm-tax-neighbor.xml" ftype="xml"/> + </test> + </tests> + <help><![CDATA[ +NCBI Entrez ELink +================= + +Responds to a list of UIDs in a given database with either a list of related +UIDs (and relevancy scores) in the same database or a list of linked UIDs in +another Entrez database; checks for the existence of a specified link from a +list of one or more UIDs; creates a hyperlink to the primary LinkOut provider +for a specific UID and database, or lists LinkOut URLs and attributes for +multiple UIDs. + +Commands +-------- + +Example Queries +--------------- + +Link from protein to gene + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | Protein | ++----------------------+--------------------------------------+ +| Elink Command | Neighbor | ++----------------------+--------------------------------------+ +| To NCBI Database | Gene | ++----------------------+--------------------------------------+ +| ID List | 15718680 157427902 | ++----------------------+--------------------------------------+ + +Find related articles to PMID 20210808 with scores + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | PubMed | ++----------------------+--------------------------------------+ +| Elink Command | Scored Neighbors | ++----------------------+--------------------------------------+ +| To NCBI Database | PubMed | ++----------------------+--------------------------------------+ +| ID List | 20210808 | ++----------------------+--------------------------------------+ + +List all possible links from two protein GIs + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | Protein | ++----------------------+--------------------------------------+ +| Elink Command | ACheck | ++----------------------+--------------------------------------+ +| ID List | 15718680 157427902 | ++----------------------+--------------------------------------+ + +List all possible links from two protein GIs to PubMed + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | Protein | ++----------------------+--------------------------------------+ +| Elink Command | ACheck | ++----------------------+--------------------------------------+ +| To NCBI Database | PubMed | ++----------------------+--------------------------------------+ +| ID List | 15718680 157427902 | ++----------------------+--------------------------------------+ + +Check whether two nuccore sequences have "related sequences" links. + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | Nuccore | ++----------------------+--------------------------------------+ +| Elink Command | NCheck | ++----------------------+--------------------------------------+ +| ID List | 21614549 219152114 | ++----------------------+--------------------------------------+ + +List the LinkOut URLs for non-library providers for two pubmed abstracts. + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | Pubmed | ++----------------------+--------------------------------------+ +| Elink Command | Links | ++----------------------+--------------------------------------+ +| ID List | 19880848 19822630 | ++----------------------+--------------------------------------+ + +Find links to full text providers for two PubMed abstracts. + ++----------------------+--------------------------------------+ +| Parameter | Value | ++======================+======================================+ +| From NCBI Database | Pubmed | ++----------------------+--------------------------------------+ +| Elink Command | Provider Links | ++----------------------+--------------------------------------+ +| ID List | 19880848 19822630 | ++----------------------+--------------------------------------+ + +@REFERENCES@ + +@DISCLAIMER@ + ]]></help> + <expand macro="citations"/> +</tool>