diff bih4bloodexposome.xml @ 0:94eeed7f737f draft default tip

planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29

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+++ b/bih4bloodexposome.xml	Fri Nov 27 10:06:35 2020 +0000
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+<tool id="bih4bloodexposome" name="BiH4BloodExposome" version="0.1.2">
+  <description>
+	: Utility to detect potential metabolites known or suspected to be part of blood exposome in your peak list.
+  </description>
+  <requirements>
+  	<requirement type="package" version="0.6.3">perl-metabolomics-fragment-annotation</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1" level="fatal" />
+  </stdio>
+  
+  <command><![CDATA[
+         perl $__tool_directory__/bih4bloodexposome.pl
+         -input $variableMetadata_in
+         -mzCol $colmass
+
+         #if str($has_header.header_choice) == "YES":
+          -header "${has_header.header}"
+         #end if
+
+         -ppmError $ppm_error
+         -mode $mode
+         -outputTab $outputTab
+         -outputFull $outFull
+         -verbose $verbose
+  ]]></command>
+  <inputs>
+        <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" />
+    
+    	<conditional name="has_header">
+    		<param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" />
+        	<when value="YES">
+        		<param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/>
+        	</when>
+        	<when value="NO"/>
+    	</conditional>
+    
+    	<param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
+        
+      <param name="verbose" type="select" label="Verbose level" display="radio" help="">
+	        <option value="1" selected="true">Low</option>
+        	<option value="3" >High</option>
+	  </param>
+      
+
+      <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/>
+
+      <param name="mode" label="Molecular Species " type="select" display="radio" help="">
+        <option value="POSITIVE">Positif Mode</option>
+        <option value="NEGATIVE">Negatif Mode</option>
+        <option value="NEUTRAL">Neutral Mass</option>
+      </param> 
+
+  </inputs>
+  <outputs>
+    <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4BLOODEXPOSOME_Full.tabular" />
+    <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4BLOODEXPOSOME.tabular" />
+  </outputs>
+  <tests>
+    <!--test 01 : short input id, mz and rt data -->
+    <test>
+      <param name="variableMetadata_in" value="in_test01_pos.tabular"/>
+      <param name="header_choice" value="YES"/>
+      <param name="header" value="1"/>
+      <param name="colmass" value="2"/>
+      <param name="ppm_error" value="5"/>
+      <param name="mode" value="POSITIVE"/>
+      <param name="verbose" value="3"/>
+      <output name="outFull" file="outFull_test01.tabular"/>
+      <output name="outputTab" file="outTab_test01.tabular"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+
+.. class:: infomark
+
+**Authors**
+  | Franck Giacomoni - FLAME ; PFEM ; INRAE ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) - based on the Perl CPAN package Metabolomics::Fragmentation::Annotation
+
+---------------------------------------------------
+
+
+======================
+bih4BloodExposome
+======================
+
+-----------
+Description
+-----------
+
+ | detection of potential metabolites in your peak list based on BloodExposome database
+
+
+Keywords
+========
+
+blood, metabolite, exposome
+
+
+-----------
+Input files
+-----------
+
+
++--------------------------------+-----------+
+| Parameter : num + label        |  Format   |
++================================+===========+
+| 1 : File with a list 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 tabular input file
+    |
+
+
+----------
+Parameters
+----------
+
+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 mz in the tabular input file
+    |
+
+
+In all cases :
+
+PPM error 
+    | Specify a delta (in ppm) to apply on annotating mass - This value is a float.
+    |
+
+
+------------
+Output files
+------------
+
+Two types of files (if you manually enter the masses both files are mingled):
+    | BIH4BLOODEXPOSOME_(input.name)_FULL.tabular : for linking with others modules.
+    | BIH4BLOODEXPOSOME_(input.name).tabular : an excel-like output will be available. 
+    | 
+
+
+---------------------------------------------------
+
+---------------
+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 2019":
+ | Using Galaxy4Metabolomics - W4M table format for Galaxy
+ | Annotation Banks - Annotation  
+  
+  ]]></help>
+    <citations>
+    <citation type="doi">10.1289/EHP4713</citation>
+  </citations>
+</tool>
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