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Init repository with last massbank_ws_searchspectrum master version
author fgiacomoni
date Wed, 19 Apr 2017 11:31:58 -0400
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<tool id="massbank_ws_searchspectrum" name="MassBank spectrum searches" version="2017-02-06">
  <description>
       : Search by pseudo-spectra on a High Quality Mass Spectral Database.
  </description>
  <requirements>
    <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="2.90">perl-json</requirement>
  </requirements>
  <stdio>
    <exit_code level="fatal" range="1"/>
  </stdio>
  <command><![CDATA[
	perl $__tool_directory__/massbank_ws_searchspectrum.pl -masses "${variableMetadata_in}" -col_mz "$col_mz" -col_pcgroup "$col_pcgroup" -score_threshold "$score_threshold"
		#if str($header.header_choice) == "true":
			-lineheader "${header.nbheader}"
		#end if
		
		#if str($intensity.colint_choice) == "true":
			-col_int "${intensity.col_int}"
		#end if
		
		#if str($mode) == "Positive,Negative":
			-mode "both"
		#else:
			-mode "$mode"
		#end if
		
		#if str($advanced.advanced_settings) == "false":
			-instruments "all" -max "10" -unit "unit" -tolerance "0.3" -cutoff "50" -server "JP"
		#else:
			-instruments "${advanced.instruments}" -max "${advanced.max}"
			-unit "${advanced.mz_tolerance.unit}" -tolerance "${advanced.mz_tolerance.tolerance}"
			-cutoff "${advanced.cutoff}" -server "${advanced.server}"
		#end if
		
		-output_tabular "$variableMetadata_out"
		-output_xlsx "$massBankSpectraOutXlsx"
		-output_json "$massBankSpectraOutJson"
		-output_html "$massBankSpectraOutWeb"

  ]]></command>
  <inputs>
    <param format="tabular" help="Generally variable metadata file" label="File of masses (format: tabular)" name="variableMetadata_in" type="data"/>
    <conditional name="header">
      <param checked="true" falsevalue="false" help="if 'YES' is selected then enter your number of header lines" label="Do you have a header?" name="header_choice" truevalue="true" type="boolean"/>
      <when value="true">
        <param help="number of lines not containing masses" label="Number of header lines" max="10" min="1" name="nbheader" type="integer" value="1"/>
      </when>
      <when value="false"/>
    </conditional>
    <param accept_default="true" data_ref="variableMetadata_in" label="Column of masses (MZ)" name="col_mz" type="data_column"/>
    <param accept_default="true" data_ref="variableMetadata_in" label="Column of pcgroup" name="col_pcgroup" type="data_column"/>
    <conditional name="intensity">
      <param checked="true" falsevalue="false" help="if 'No' is selected, the value of intensity for each mz is set to 10 (MassBank spectrum search require mz-pcgroup-intensity data - please use massbank peak search if needed)" label="Do you have a column of intensity?" name="colint_choice" truevalue="true" type="boolean"/>
      <when value="true">
        <param accept_default="true" data_ref="variableMetadata_in" label="Column of intensity" name="col_int" type="data_column"/>
      </when>
      <when value="false"/>
    </conditional>
    <param display="checkboxes" help="" label="What kind of Ionization Search will be done?" multiple="True" name="mode" type="select">
      <option selected="true" value="Positive">Positif Mode</option>
      <option selected="true" value="Negative">Negatif Mode</option>
    </param>
    <param help="Default value is 0.5." label="Score threshold to apply on returned MassBank results" max="1" min="0" name="score_threshold" type="float" value="0.5"/>
    <conditional name="advanced">
      <param checked="false" falsevalue="false" help="if 'NO' is selected then defaults values are: instruments = all ; max = 10 ; unit = unit ; tolerance = 0.3 ; cutoff = 50 ; server = JP" label="Show advanced settings?" name="advanced_settings" truevalue="true" type="boolean"/>
      <when value="true">
        <param display="checkboxes" help="" label="What kind of Instruments will be use?" multiple="True" name="instruments" type="select">
          <option selected="True" value="all">All</option>
          <option value="APCI-ITFT">APCI-ITFT</option>
          <option value="APCI-ITTOF">APCI-ITTOF</option>
          <option value="CE-ESI-TOF">CE-ESI-TOF</option>
          <option value="CI-B">CI-B</option>
          <option value="EI-B">EI-B</option>
          <option value="EI-EBEB">EI-EBEB</option>
          <option value="ESI-ITFT">ESI-ITFT</option>
          <option value="ESI-ITTOF">ESI-ITTOF</option>
          <option value="FAB-B">FAB-B</option>
          <option value="FAB-EB">FAB-EB</option>
          <option value="FAB-EBEB">FAB-EBEB</option>
          <option value="FD-B">FD-B</option>
          <option value="FI-B">FI-B</option>
          <option value="GC-EI-QQ">GC-EI-QQ</option>
          <option value="GC-EI-TOF">GC-EI-TOF</option>
          <option value="LC-APCI-QTOF">LC-APCI-QTOF</option>
          <option value="LC-APPI-QQ">LC-APPI-QQ</option>
          <option value="LC-ESI-IT">LC-ESI-IT</option>
          <option value="LC-ESI-ITFT">LC-ESI-ITFT</option>
          <option value="LC-ESI-ITTOF">LC-ESI-ITTOF</option>
          <option value="LC-ESI-Q">LC-ESI-Q</option>
          <option value="LC-ESI-QFT">LC-ESI-QFT</option>
          <option value="LC-ESI-QIT">LC-ESI-QIT</option>
          <option value="LC-ESI-QQ">LC-ESI-QQ</option>
          <option value="LC-ESI-QTOF">LC-ESI-QTOF</option>
          <option value="LC-ESI-TOF">LC-ESI-TOF</option>
          <option value="MALDI-QIT">MALDI-QIT</option>
          <option value="MALDI-TOF">MALDI-TOF</option>
          <option value="MALDI-TOFTOF">MALDI-TOFTOF</option>
        </param>
        <param help="'0' means unspecified and then all results are obtained." label="Maximum number of search results" max="50" min="0" name="max" type="integer" value="10"/>
        <conditional name="mz_tolerance">
          <param display="radio" help="" label="Unit of tolerance" name="unit" type="select">
            <option selected="True" value="unit">unit</option>
            <option value="ppm">ppm</option>
          </param>
          <when value="unit">
            <param help="Default value is 0.3 unit." label="Tolerance of values of m/z of peaks (in unit)" max="10" min="0" name="tolerance" type="float" value="0.3"/>
          </when>
          <when value="ppm">
            <param help="Default value is 50 ppm." label="Tolerance of values of m/z of peaks (in ppm)" max="5000" min="0" name="tolerance" type="integer" value="50"/>
          </when>
        </conditional>
        <param help="Ignore peaks whose intensity is not larger than the value of cutoff." label="Ignore peaks whose intensity is not larger than the value of cutoff" max="5000000" min="0" name="cutoff" type="integer" value="50"/>
        <param display="radio" help="" label="Which MassBank server start searching?" name="server" type="select">
          <option selected="True" value="JP">Japon (JP)</option>
          <option value="EU">Europe (EU)</option>
        </param>
      </when>
      <when value="false"/>
    </conditional>
  </inputs>
  <outputs>
    <data format="tabular" label="${variableMetadata_in.name[:-6]}.MASSBANK.tabular" name="variableMetadata_out"/>
    <data format="html" label="${variableMetadata_in.name[:-6]}.MASSBANK_WEB.html" name="massBankSpectraOutWeb"/>
    <data format="tabular" label="${variableMetadata_in.name[:-6]}.MASSBANK_XLS.txt" name="massBankSpectraOutXlsx"/>
    <data format="txt" label="${variableMetadata_in.name[:-6]}.MASSBANK_JSON.txt" name="massBankSpectraOutJson"/>
  </outputs>
  <tests>
    <test>
      <!--test 01 short result -  -->
      <param name="variableMetadata_in" value="input01_69-pcgroups-mz-relative_int.tabular"/>
      <param name="header" value="true"/>
      <param name="nbheader" value="1"/>
      <param name="col_mz" value="1"/>
      <param name="col_pcgroup" value="14"/>
      <param name="colint_choice" value="true"/>
      <param name="col_int" value="7"/>
      <param name="mode" value="Positive"/>
      <param name="score_threshold" value="0.5"/>
      <param name="advanced_settings" value="true"/>
      <param name="instruments" value="all"/>
      <param name="max" value="20"/>
      <param name="unit" value="unit"/>
      <param name="tolerance" value="0.3"/>
      <param name="cutoff" value="50"/>
      <param name="server" value="JP"/>
      <output file="out_test01.tabular" name="variableMetadata_out"/>
      <output file="out_test01.html" name="massBankSpectraOutWeb"/>
      <output file="out_test01.txt" name="massBankSpectraOutXlsx"/>
      <!--<output file="out_test01.json" name="massBankSpectraOutJson"/> The JSON output structure is messy, so it is delete from test-->
    </test>
    <!--t<test>
  	</test>
    <test>
  	</test>-->
  </tests>
  <help><![CDATA[

.. class:: infomark

**Wrapping**
  | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface and perl wrapper and WS client)

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

.. class:: infomark

**Please cite** If you use this tool, please cite MassBank (http://www.massbank.jp)


==============
wsdl_MassBank
==============

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

Finding information (search spectra method) in the MassBank project via a web service from masses and pcgroups.

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


.. image:: ./static/images/metabolomics/massbank-ws.png
        :width: 800


-----------
Input files
-----------

+-------------------------+-----------+
| Parameter : num + label |  Format   |
+=========================+===========+
| 1 : variableMetadata    |  tabular  |
+-------------------------+-----------+

File variableMetadata must have at least the 3 following column : 
	* Masses : column with all the masses in the tabular input file
	* Intensities : column with all the intensities in the tabular input file (Optionnal but if you haven't intensitt values, please use the Massbank peak search tool)
	* PCgroups : column with all the pcgroups in the tabular input file


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

Number of header lines
	| Number of lines not containing values 
	|

Column of masses
	| Specify the column number for the mass in the tabular input file
	|

Tolerance of mass (in unit or ppm)
	| Specify a delta (+/-) to the mass to search
	
Parameters applied on query
	| cutoff : intensity cutoff (don't add to the query, mz with intensity below defined cutoff).
	| max: maximum number of records returned by the MASSBANK server foreach pcgroup of masses (by default max is set to 10).
	| score_threshold: apply a filter on MASSBANK scores (by default threshold is set to 0.5).
	| mode : Ionization search mode: Positive or Negative ou Both
	| Instrument: filter applied on spectra depending of the instrument source. (All is the default value) - - GCMS technologies are available in W4M GCMS tools section.

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

Two types of files
	| MASSBANK_WEB.html: for viewing result via HTML.
	| MASSBANK.tabular: for linking with others modules.
	| MASSBANK_XLS.txt: an excel-like output to export results under a multi lines format.
	| MASSBANK_JSON.txt: an json 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 2016":
 | 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">10.1002/jms.1777</citation>
  </citations>
</tool>