view efetch.xml @ 3:c09fcbe4b16a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"

<?xml version="1.0"?>
<tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
  <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"><![CDATA[

    python '$__tool_directory__/efetch.py'

    $db.db_select

    @LIST_OR_HIST@

    @EMAIL_ARGUMENTS@

    @EFETCH_FORMAT_TOKEN@

]]></command>
  <inputs>
    <expand macro="list_or_hist"/>
    <expand macro="efetchdb"/>
  </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="none-xml-xml"/>
      <param name="qss" value="id_list"/>
      <param name="id_list" value="10239"/>
      <output_collection name="output1" type="list" count="1">
        <element name="EFetch-None-xml-chunk1" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
      </output_collection>
    </test>
    <test>
      <param name="db_select" value="nuccore"/>
      <param name="output_format" value="fasta-text-fasta"/>
      <param name="qss" value="id_file"/>
      <param name="id_file" value="efetchin.tabular"/>
      <output_collection name="output1" type="list" count="1">
        <element name="EFetch-fasta-text-chunk1" ftype="xml" file="efetch.tabin.fasta" />
      </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>