annotate downloader_bank_hmdb.xml @ 0:7c9269bded0e draft

Init repository for [downloader_bank_hmdb]

<tool id="downloader_bank_hmdb" name="HMDB bank downloader" version="2018.12">
  <description>
        : get a specific metabolite bank (as Urine...) from HMDB web portal.
  </description>
  
  <requirements>
      <requirement type="package" version="2.161">perl-data-dumper</requirement>
      <requirement type="package" version="6.15">perl-lwp-simple</requirement>
	  <requirement type="package" version="6.15">perl-libwww-perl</requirement>
      <requirement type="package" version="1.74">perl-uri</requirement>
      <requirement type="package" version="1.97">perl-text-csv</requirement>
      <requirement type="package" version="3.52">perl-xml-twig</requirement>
      <requirement type="package" version="1.60">perl-archive-zip</requirement>
      <requirement type="package" version="2.064">perl-io-uncompress-gunzip</requirement>
  </requirements>
  
  <stdio>
      <exit_code range="1" level="fatal" />
  </stdio>
  
  
  <command><![CDATA[
        perl $__tool_directory__/downloader_bank_hmdb.pl
            -bank "$bank"
            -verbose "$verbose"
            -format "$bankformat"
            -outTab "$outTab"
        
  ]]></command>
  <inputs>
  	<param name="bank" type="select" label="What is the specific bank you want to download? " help="All banks are extracted from downloads section on HMDB web portal.">
        <option value="SERUM" selected="true">Human serum</option>
        <option value="URINE">Human urine</option>
        <option value="CSF">Human cerebrospinal fluid</option>
        <option value="FECES">Human feces</option>
        <option value="SALIVA">Human saliva</option>
        <option value="COW">Bovine</option>
        <option value="RUMEN">Bovine rumen</option>
        <option value="MILK">Bovine milk</option>
    </param>
    <param name="bankformat" type="select" label="Which output format do you need? " help="Proposed formats are lighter than downloaded raw files and adapted to annotation tools.">
        <option value="tabular" selected="true">tabular (for BiH tool)</option>
        <!--<option value="json">json (still in construction)</option>-->
    </param>
    <param name="verbose" type="select" label="Level of script verbose " help="Information about script running.">
        <option value="1" selected="true">low</option>
        <option value="3">high</option>
    </param>
  </inputs>
  
  <outputs>
    <data name="outTab" format="tabular" label="REF_HMDB_${bank}.tabular"/>
    <!--<data name="outJson" format="json" label="REF_HMDB_${bank}.json"/>-->
  </outputs>
  
  <tests>
  	<test>
  		<!--test 01 CSF download and produce a simple tabular -->
  		<param name="bank" value="CSF"/>
  		<param name="bankformat" value="tabular"/>
  		<param name="verbose" value="1"/>
  		<output name="outTab" file="out01.tabular"/>
  	</test>
  </tests>

  <help><![CDATA[

.. class:: infomark

**Authors** Charlotte Joly, Delphine Centeno and Franck Giacomoni

---------------------------------------------------

.. class:: infomark

**Please cite** If you use this tool, please add the following reference
  | Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018. Jan 4;46(D1):D608-17.


---------------------------------------------------

====================
HMDB bank downloader
====================

-----------
Description
-----------

 | Download a bank containing information (like : HMDB id,  Name, mz, inchikey) 
 | from HMDB online web portal and convert it into W4M annotation tool input formats.
 |


-----------------
Workflow position
-----------------


.. image:: ./static/images/metabolomics/hmdb.png
        :width: 800



----------
Parameters
----------

What is the specific bank you want to download
	| Choose whether specific metabolite banks:
	| Urine
	| Serum
	| cerebrospinal fluid
	| ...
	|


Which output format do you need
	| tabular : for W4M BiH annotation tool as example
	| json : still in construction
	|



------------
Output files
------------

Two types of files
	| REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example
	| 
	| REF_HMDB_BANKNAME.json: for linking with others modules.
	|
	
---------------------------------------------------


---------------
Working example
---------------


.. class:: warningmark

Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
 | Format Data For Postprocessing
 | Perform LCMS Annotations

.. class:: warningmark

And their "W4M courses 2018":
 | Using Galaxy4Metabolomics - W4M table format for Galaxy
 | Annotation Banks - Annotation  
	

	]]></help>
	<!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
  <citations>
    <citation type="doi">10.1093/nar/gkx1089</citation>
  </citations>
</tool>