Mercurial > repos > fgiacomoni > hmdb_ms_search

diff wsdl_hmdb.xml @ 21:63ba1cb240b7 draft

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Prod branch Updating - - Fxx
author fgiacomoni
date Thu, 14 Feb 2019 08:36:52 -0500
parents ec7c05889e67
children 453fbe98925a
line wrap: on
line diff
--- a/wsdl_hmdb.xml	Wed Jan 23 07:49:34 2019 -0500
+++ b/wsdl_hmdb.xml	Thu Feb 14 08:36:52 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.0">
+<tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.1">
   <description>
         search by masses on HMDB online LCMS bank
   </description>
@@ -8,10 +8,11 @@
       <requirement type="package" version="2.97">perl-html-template</requirement>
       <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="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="1.91">perl-www-mechanize</requirement>
   </requirements>
   
   <stdio>
@@ -33,7 +34,18 @@
             -mass "${input_type.mass}"
             -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
         #end if
-        -delta "$delta" -mode "$mode" -maxquery "$maxquery"
+        
+        -mode "${mode_type.mode}"
+        
+        #if str($mode_type.mode) == "positive":
+        	-adduct_type "${mode_type.data_positive_adducts}"
+        #elif str($mode_type.mode) == "negative":
+        	-adduct_type "${mode_type.data_negative_adducts}"
+        #elif str($mode_type.mode) == "neutral":
+        	-adduct_type "${mode_type.data_neutral_adducts}"
+        #end if
+        
+        -delta "$delta" -maxquery "$maxquery"
         -advancedFeatures "$advancedFeatures"
         -verbose "$verbose"
         
@@ -64,12 +76,91 @@
     </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>
+    <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="10" min="1" max="50" size="10" help="Default value is 10 for each queried mz / max is 50"/>
+    
+    <conditional name="mode_type">
+    	<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>
+    	<when value="positive">
+    		<param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
+    			<option value="Unknown">Unknown</option>
+    			<option value="M+H" selected="True">M+H</option>
+    			<option value="M+H-2H2O">M+H-2H2O</option>
+    			<option value="M+H-H2O">M+H-H2O</option>
+    			<option value="M+NH4-H2O">M+NH4-H2O</option>
+    			<option value="M+Li">M+Li</option>
+    			<option value="M+NH4">M+NH4</option>
+    			<option value="M+Na">M+Na</option>
+    			<option value="M+CH3OH+H">M+CH3OH+H</option>
+    			<option value="M+K">M+K</option>
+    			<option value="M+ACN+H">M+ACN+H</option>
+    			<option value="M+2Na-H">M+2Na-H</option>
+    			<option value="M+IsoProp+H">M+IsoProp+H</option>
+    			<option value="M+ACN+Na">M+ACN+Na</option>
+    			<option value="M+2K-H">M+2K-H</option>
+    			<option value="M+DMSO+H">M+DMSO+H</option>
+    			<option value="M+2ACN+H">M+2ACN+H</option>
+    			<option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option>
+    			<option value="M+H+HCOONa">M+H+HCOONa</option>
+    			<option value="2M+H">2M+H</option>
+    			<option value="2M+NH4">2M+NH4</option>
+    			<option value="2M+Na">2M+Na</option>
+    			<option value="2M+2H+3H2O">2M+2H+3H2O</option>
+    			<option value="2M+K">2M+K</option>
+    			<option value="2M+ACN+H">2M+ACN+H</option>
+    			<option value="2M+ACN+Na">2M+ACN+Na</option>
+    			<option value="2M+H-H2O">2M+H-H2O</option>
+    			<option value="M+2H">M+2H</option>
+    			<option value="M+H+NH4">M+H+NH4</option>
+    			<option value="M+H+Na">M+H+Na</option>
+    			<option value="M+H+K">M+H+K</option>
+    			<option value="M+ACN+2H">M+ACN+2H</option>
+    			<option value="M+2Na">M+2Na</option>
+    			<option value="M+2ACN+2H">M+2ACN+2H</option>
+    			<option value="M+3ACN+2H">M+3ACN+2H</option>
+    			<option value="M+3H">M+3H</option>
+    			<option value="M+2H+Na">M+2H+Na</option>
+    			<option value="M+H+2Na">M+H+2Na</option>
+    			<option value="M+3Na">M+3Na</option>
+    			<option value="M+H+2K">M+H+2K</option>
+    		</param>
+    	</when>
+    	<when value="negative">
+    		<param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
+    			<option value="Unknown">Unknown</option>
+    			<option value="M-H" selected="True">M-H</option>
+    			<option value="M-H20-H">M-H20-H</option>
+    			<option value="M+F">M+F</option>
+    			<option value="M+Na-2H">M+Na-2H</option>
+    			<option value="M+Cl">M+Cl</option>
+    			<option value="M+K-2H">M+K-2H</option>
+    			<option value="M+FA-H">M+FA-H</option>
+    			<option value="M+Hac-H">M+Hac-H</option>
+    			<option value="M+Br">M+Br</option>
+    			<option value="M+TFA-H">M+TFA-H</option>
+    			<option value="M-H+HCOONa">M-H+HCOONa</option>
+    			<option value="2M-H">2M-H</option>
+    			<option value="2M+FA-H">2M+FA-H</option>
+    			<option value="2M+Hac-H">2M+Hac-H</option>
+    			<option value="3M-H">3M-H</option>
+    			<option value="M-2H">M-2H</option>
+    			<option value="M-3H">M-3H</option>
+    		</param>
+    	</when>
+    	<when value="neutral">
+    		<param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
+    			<option value="Unknown">Unknown</option>
+    			<option value="M" selected="True">M</option>
+    		</param>
+    	</when>
+    </conditional>
+    
+    
+    
+    
     <param name="advancedFeatures" label="Performing advanced annotation " type="select" display="radio" help="Getting more information from HMDB (Inchi, logP, ...) but increase time of tool execution">
       <option value="1">Advanced mode</option>
       <option value="0" selected="True">Default mode</option>