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+++ b/downloader_bank_hmdb.xml	Tue Jan 14 05:21:23 2020 -0500
@@ -0,0 +1,161 @@
+<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>
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