diff wsdl_hmdb.xml @ 1:6d0a0f8f672a draft

planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471

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+++ b/wsdl_hmdb.xml	Wed Nov 23 09:31:50 2016 -0500
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+<tool id="wsdl_hmdb" name="HMDB MS search" version="2016-11-28">
+  <description>
+        search by masses on HMDB online bank
+  </description>
+  
+  <requirements>
+  <!-- Waiting for conda improvement in Galaxy
+      <requirement type="package" version="1.19">perl-soap-lite</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="2.95">perl-html-template</requirement>
+      <requirement type="package" version="1.71">perl-uri</requirement>
+      <requirement type="package" version="1.33">perl-text-csv</requirement>
+      <requirement type="package" version="3.49">perl-xml-twig</requirement>
+  -->
+  </requirements>
+  
+  <stdio>
+      <exit_code range="1" level="fatal" />
+  </stdio>
+  
+  
+  <command><![CDATA[
+        perl $__tool_directory__/wsdl_hmdb.pl
+        #if str($input_type.choice) == "YES":
+            -masses "${input_type.masses}"
+            -header_choice "${input_type.header.header_choice}"
+            #if str($input_type.header.header_choice) == "yes":
+                -nblineheader "${$input_type.header.nbHeader}"
+            #end if
+            -colfactor "${input_type.colfactor}"
+            -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx"
+        #else:
+            -mass "${input_type.mass}"
+            -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
+        #end if
+        -delta "$delta" -mode "$mode" -maxquery "$maxquery"
+        
+  ]]></command>
+  <inputs>
+    <conditional name="input_type">
+      <param name="choice" type="select" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually">
+        <option value="YES">YES</option>
+        <option value="NO">NO</option>
+      </param>
+      <when value="YES">
+        <param name="masses" label="File of masses (Variable Metadata) " format="tabular" type="data" help="Generally variable metadata file. Please note : HMDB allows maximum 150 query masses per request" />
+        <conditional name="header">
+          <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines">
+            <option value="no">NO</option>
+            <option value="yes" selected="true">YES</option>
+          </param>
+          <when value="yes">
+            <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/>
+          </when>
+          <when value="no"/>
+        </conditional>
+	    <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
+      </when>
+      <when value="NO">
+        <param name="mass" label="Mass to submit " type="text" size="20" help="For a masses list, writes : m1 m2 m3. Your values ​​must be separated by spaces. You should use dot (.) like decimal separator" />
+      </when>
+    </conditional>
+    
+    <param name="delta" label="Mass-to-charge ratio " type="float" value="0.05" min="0" max="10" size="10" help="Default value is 0.05 for HMDB (mass-to-charge ratio)"/>
+    <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="20" min="1" max="50" size="10" help="Default value is 20 for each queried mz / max is 50"/>
+    <param name="mode" label="Molecular Species " type="select" display="radio" help="">
+      <option value="positive">Positif Mode</option>
+      <option value="negative">Negatif Mode</option>
+      <option value="neutral" selected="True">Neutral Mass</option>
+    </param>
+  </inputs>
+  
+  <outputs>
+    <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
+    	<filter>input_type['choice'] == "YES"</filter>
+   	</data>
+    <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
+    	<filter>input_type['choice'] == "YES"</filter>
+   	</data>
+    <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB.xlsx" format="tabular">
+    	<filter>input_type['choice'] == "YES"</filter>
+   	</data>
+    <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
+    	<filter>input_type['choice'] == "NO"</filter>
+   	</data>
+    <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
+    	<filter>input_type['choice'] == "NO"</filter>
+   	</data>
+    <data name="HmdbOutXlsx2" label="HMDB.xlsx" format="tabular">
+    	<filter>input_type['choice'] == "NO"</filter>
+   	</data>
+  </outputs>
+  
+  <tests>
+  	<test>
+  		<!--test 01 no result - fake-mzrt-input-with-id -->
+  		<param name="choice" value="YES"/>
+  		<param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
+  		<param name="header_choice" value="yes"/>
+  		<param name="nblineheader" value="1"/>
+  		<param name="colfactor" value="2"/>
+  		<param name="delta" value="0.001"/>
+  		<param name="mode" value="neutral"/>
+  		<param name="maxquery" value="5"/>
+  		<output name="variableMetadata" file="out_test01.tabular"/>
+  		<output name="HmdbOutWeb" file="out_test01.html"/>
+  		<output name="HmdbOutXlsx" file="out_test01.xlsx"/>
+  	</test>
+  	<test>
+  		<!--test 02 : some results - with-mzrt-input-with-id file-->
+  		<param name="choice" value="YES"/>
+  		<param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
+  		<param name="header_choice" value="yes"/>
+  		<param name="nblineheader" value="1"/>
+  		<param name="colfactor" value="2"/>
+  		<param name="delta" value="0.001"/>
+  		<param name="mode" value="positive"/>
+  		<param name="maxquery" value="5"/>
+  		<output name="variableMetadata" file="out_test02.tabular"/>
+  		<output name="HmdbOutWeb" file="out_test02.html"/>
+  		<output name="HmdbOutXlsx" file="out_test02.xlsx"/>
+  	</test>
+  	<test>
+  		<!--test 03 : some results - with-mz list in manual mass mode-->
+  		<param name="choice" value="NO"/>
+  		<param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
+  		<param name="delta" value="0.05"/>
+  		<param name="mode" value="positive"/>
+  		<param name="maxquery" value="5"/>
+  		<output name="variableMetadata2" file="out_test03.tabular"/>
+  		<output name="HmdbOutWeb2" file="out_test03.html"/>
+  		<output name="HmdbOutXlsx2" file="out_test03.xlsx"/>
+  	</test>
+  </tests>
+
+  <help><![CDATA[
+
+.. class:: infomark
+
+**Authors** Marion Landi and Franck Giacomoni
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Please cite** If you use this tool, please add the following reference
+  | Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013.
+
+
+---------------------------------------------------
+
+==============
+HMDB MS search
+==============
+
+-----------
+Description
+-----------
+
+ | Search informations (like : HMDB id,  Name, Adduct, delta mass) on HMDB online bank
+ | with one or more mass(es) in a file or entered manually
+
+
+-----------------
+Workflow position
+-----------------
+
+
+.. image:: ./static/images/metabolomics/hmdb.png
+        :width: 800
+
+
+-----------
+Input files
+-----------
+
+
++-------------------------+-----------+
+| Parameter : num + label |  Format   |
++=========================+===========+
+| 1 : File of masses      |  tabular  |
++-------------------------+-----------+
+
+File of masses (Generally variable metadata file) must have at least the following column : 
+	* Masses : column with all the masses in the tsv input file
+
+----------
+Parameters
+----------
+
+Would you use a file
+	| Choose whether the masses are in a file or entered manually
+	| YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible
+	| NO : parameter **Mass to submit** is visible
+	|
+
+
+If 'use file'='YES'
+
+File of masses
+	| see "Input files" section above
+	| Tabular file format, Generally variable metadata file
+	| 
+
+Do you have a header
+	| YES (default) : parameter **Number of header lines** is visible
+	| NO : all lines are considered to contain masses
+	|
+
+If 'have a header'='YES'
+
+Number of header lines
+	| Number of lines not containing masses values, these lines will be ignored
+	|
+
+In all header cases :
+
+Column of masses
+	| Specify the column number for the mass in the tsv input file
+	|
+
+
+If 'use file'='NO'
+
+Mass to submit
+	| Specify a list of mass to request
+	| one or more mass(es) entered manually
+	| For a masses list, writes : m1 m2 m3
+	| You must separate yours values with space
+	| dot (.) is for float number
+	|
+
+In all cases :
+
+Mass-to-charge ratio
+	| Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10.
+	|
+
+Molecular Species
+	| Type of ionization of the molecule : *positif, negatif, neutral*
+	|
+
+
+------------
+Output files
+------------
+
+Two types of files
+	| HMDB_WEB.HTML: for viewing result via HTML.
+	| 
+	| HMDB_TABULAR.tabular: for linking with others modules.
+	| 
+	| HMDB_XLSX.xlsx: an excel-like output permitting manual annotation cleaning. 
+	| 
+	
+---------------------------------------------------
+
+
+---------------
+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 2015":
+ | Using Galaxy4Metabolomics - W4M table format for Galaxy
+ | Annotation Banks - Annotation  
+	
+
+	]]></help>
+</tool>
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