annotate efetch.xml @ 1:0fc65a60436f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed

<?xml version="1.0"?>
<tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@">
  <description>fetch records from NCBI</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python efetch.py --version</version_command>
  <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
$db.db_select

@LIST_OR_HIST@

#set rettype, retmode = str($db.output_format).split('-')
## Otherwise, defaults to a None/empty which implies 'default' to NCBI
#if retmode != "null":
--retmode $retmode
#end if
--rettype $rettype

@EMAIL_ARGUMENTS@
]]></command>
  <inputs>
    <expand macro="db"/>
    <expand macro="list_or_hist"/>
  </inputs>
  <outputs>
    <collection name="output1" type="list" label="NCBI EFetch results">
      <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
    </collection>
  </outputs>
  <tests>
    <test>
      <param name="db_select" value="taxonomy"/>
      <param name="output_format" value="full-xml"/>
      <param name="qss" value="id_list"/>
      <param name="id_list" value="10239"/>
      <output_collection name="output1" type="list" count="1">
        <element name="EFetch Results Chunk 0" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
      </output_collection>
    </test>
  </tests>
  <help><![CDATA[
NCBI Entrez EFetch
==================

Responds to a list of UIDs in a given database with the corresponding data
records in a specified format.

Example Queries
---------------

Fetch PMIDs 17284678 and 9997 as text abstracts:

+----------------------+--------------------------------------+
| Parameter            | Value                                |
+======================+======================================+
| NCBI Database to Use | PubMed                               |
+----------------------+--------------------------------------+
| ID List              | 17284678 9997                        |
+----------------------+--------------------------------------+
| Output Format        | Abstract                             |
+----------------------+--------------------------------------+

Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)

+----------------------+--------------------------------------+
| Parameter            | Value                                |
+======================+======================================+
| NCBI Database to Use | Protein                              |
+----------------------+--------------------------------------+
| ID List              | 312836839 34577063                   |
+----------------------+--------------------------------------+
| Output Format        | Fasta                                |
+----------------------+--------------------------------------+

@REFERENCES@

@DISCLAIMER@
      ]]></help>
  <expand macro="citations"/>
</tool>