annotate elink.xml @ 2:1ed9a99b9b1f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"

<?xml version="1.0"?>
<tool id="ncbi_eutils_elink" name="NCBI ELink" version="@WRAPPER_VERSION@" profile="@PROFILE@">
  <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"><![CDATA[
python '$__tool_directory__/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>