comparison HR2.xml @ 2:23970530a518 draft

master branch Updating with tag :CI_COMMIT_TAG - - Fxx

1:e2cbcf6fa22e

<tool id="hr2" name="HR2 formula" version="1.1.2">
  <description>
        find a chemical formula from a accurate mass
  </description>
  <requirements>
      <requirement type="package" version="2.161">perl-data-dumper</requirement>

  <command><![CDATA[
        perl $__tool_directory__/hr2_manager.pl
    #if str($input_type.choice) == "YES":
        -input "${input_type.input}"
        #if str($input_type.header.header_choice) == "yes":
            -nblineheader "${$input_type.header.nbHeader}"
        #end if
        -colId "${input_type.colId}" -colmass "${input_type.colmass}"
    #else: 
        -masse "${input_type.masse}"
    #end if

            <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="colId" label="Column of Id" type="data_column" data_ref="input" accept_default="true" />
        <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="input" accept_default="true" />
      </when>
      <when value="NO">
        <param name="masse" size="20" type="text" label="Mass (MZ) to submit"  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="tol" label="Delta of mass (MZ) (in mmu)" type="float" value="1.0" min="0" max="9.0" help="Tolerance should be between 0 and 9.0 mmu. Default value is 1.0 mmu"/>
    <conditional name="mode_condition">
      <param name="mode" label="Molecular Species Searched" type="select" display="radio" help="Or ionization type of the molecule list. Use neutral only if only if the masses correspond to molecules and not to ions : query doesn't be a [M+H] or [M-H] ion">
        <option value="positive">positive</option>
        <option value="negative">negative</option>
        <option value="neutral" selected="true">neutral</option>

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Workflow position
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.. image:: ./static/images/metabolomics/hr2.png
        :width: 800

2:23970530a518

<tool id="hr2" name="HR2 formula" version="1.1.3">
  <description>
        find a chemical formula from a accurate mass
  </description>
  <requirements>
      <requirement type="package" version="2.161">perl-data-dumper</requirement>

  <command><![CDATA[
        perl $__tool_directory__/hr2_manager.pl
    #if str($input_type.choice) == "YES":
        -input "${input_type.input}"
        #if str($input_type.header.header_choice) == "yes":
            -nbHeader "${$input_type.header.nbHeader}"
        #end if
        -colId "${input_type.colId}" -colmass "${input_type.colmass}"
    #else: 
        -masse "${input_type.masse}"
    #end if

            <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="colId" label="Column of Id" type="data_column" data_ref="input" accept_default="true" />
        <param name="colmass" label="Column of masses (mz)" type="data_column" data_ref="input" accept_default="true" />
      </when>
      <when value="NO">
        <param name="masse" size="20" type="text" label="Mass (mz) to submit"  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="tol" label="Delta of mass  " type="float" value="1.0" min="0" max="9.0" help="Tolerance should be between 0 and 9.0 Da. Default value is 1.0 mmu"/>
    <conditional name="mode_condition">
      <param name="mode" label="Molecular Species Searched" type="select" display="radio" help="Or ionization type of the molecule list. Use neutral only if only if the masses correspond to molecules and not to ions : query doesn't be a [M+H] or [M-H] ion">
        <option value="positive">positive</option>
        <option value="negative">negative</option>
        <option value="neutral" selected="true">neutral</option>

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


.. image:: hr2.png
        :width: 800