annotate HR2.xml @ 3:78afd7f439f3 draft default tip

master branch Updating with tag :CI_COMMIT_TAG - - Fxx

<tool id="hr2" name="HR2 formula" version="1.2.0">
  <description>
        find a chemical formula from a accurate mass
  </description>
  <requirements>
      <requirement type="package" version="2.161">perl-data-dumper</requirement>
      <requirement type="package" version="1.97">perl-text-csv</requirement>
      <requirement type="package" version="2.97">perl-html-template</requirement>
      <requirement type="package" version="1.04">hr2</requirement>
  </requirements>
  <stdio>
      <exit_code range="1" level="fatal" />
  </stdio>
  
  
  <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
    
    -tolerance "$tol"
    -mode "${mode_condition.mode}"
    #if str($mode_condition.mode) == "neutral":
        -charge "0"
    #else:
        -charge "${mode_condition.qtCharge}"
    #end if
    
    -regleOr "$regleOr" -atomes_basic "$atomes_basic" -atomes_sup "$atomes_sup"
    
    #if str($max_custom_atom_condition.max_custom_atom_choice) == "YES":
    	-C12_max_value "${max_custom_atom_condition.C12_max_value}"
    	-C13_max_value "${max_custom_atom_condition.C13_max_value}"
    	-H_max_value "${max_custom_atom_condition.H_max_value}"
    	-N_max_value "${max_custom_atom_condition.N_max_value}"
    	-O_max_value "${max_custom_atom_condition.O_max_value}"
    	-P_max_value "${max_custom_atom_condition.P_max_value}"
    	-S_max_value "${max_custom_atom_condition.S_max_value}"
    	-F_max_value "${max_custom_atom_condition.F_max_value}"
    	-Cl_max_value "${max_custom_atom_condition.Cl_max_value}"
    	-K_max_value "${max_custom_atom_condition.K_max_value}"
    	-Br_max_value "${max_custom_atom_condition.Br_max_value}"
    	-Na_max_value "${max_custom_atom_condition.Na_max_value}"
    	
    #end if
    
    -output1 "$variableMetadata" -outputView "$hr2ResView"
    -verbose "$verbose"
  ]]></command>
  <!--     	-customAtomValues "-C 0-${max_custom_atom_condition.C12_max_value} -1 0-${max_custom_atom_condition.C13_max_value} -H 0-${max_custom_atom_condition.H_max_value} -N 0-${max_custom_atom_condition.N_max_value} -O 0-${max_custom_atom_condition.O_max_value} -P 0-${max_custom_atom_condition.P_max_value} -S 0-${max_custom_atom_condition.S_max_value} -F 0-${max_custom_atom_condition.F_max_value} -L 0-${max_custom_atom_condition.Cl_max_value} -K 0-${max_custom_atom_condition.K_max_value} -B 0-${max_custom_atom_condition.Br_max_value} -A 0-${max_custom_atom_condition.Na_max_value}"  -->
  
  <inputs>
  	<conditional name="input_type">
      <param name="choice" type="select" display="radio" 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="input" label="File of masses" format="tabular" type="data" />
        <conditional name="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="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>
      </param>
      <when value="neutral"/>
      <when value="positive">
        <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged">
          <option value="1">1</option>
          <option value="2">2</option>
          <option value="3">3</option>
        </param>
      </when>
      <when value="negative">
        <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged">
          <option value="1">1</option>
          <option value="2">2</option>
          <option value="3">3</option>
        </param>
      </when>
    </conditional>
    <param name="atomes_basic" label="Please unselect basic atom(s) from following list you want to exclude" type="select" display="checkboxes" multiple="True" help="Unselect one or more basic atoms to exclude them from the generated formula proposition">
      <option value="C" selected="true">C</option>
      <option value="N" selected="true">N</option>
      <option value="O" selected="true">O</option>
      <option value="H" selected="true">H</option>
      <option value="P" selected="true">P</option>
    </param>
    <param name="regleOr" label="Use all 7 golden rules OR only the first 3 golden rules?" type="select" display="radio" help="Use 'only first 3 rules' if you want more empirical formulas">
      <option value="YES">only first 3 rules</option>
      <option value="NO" selected="true">all 7 rules</option>
    </param>
    <param name="atomes_sup" label="Add some atom(s) from following list if needed" type="select" display="checkboxes" multiple="True" help="C, H, N, O and P are available in basic atom section">
      <option value="S">S</option>
      <option value="F">F</option>
      <option value="L">Cl</option>
      <option value="K">K</option>
      <option value="B">Br</option>
      <option value="A">Na</option>
      <option value="1">13C</option>
    </param>
    <conditional name="max_custom_atom_condition">
      <param name="max_custom_atom_choice" label="Do you want to manage custom maximum number atoms?" type="select" display="radio" help="To work only with [13]C isotopes for example, use YES - ()Don't forget to select wanted atoms below)">
        <option value="NO" selected="true">NO</option>
        <option value="YES">YES</option>
      </param>
      <when value="YES">
        <param name="C12_max_value" label="[12]C atom max number " type="integer" value="0" min="0" max="100" help="The maximum of [12]C you need to (should be between 0 and 100 atoms per structure). Default value is 0"/>
        <param name="C13_max_value" label="[13]C atom max number " type="integer" value="40" min="0" max="100" help="The maximum of [13]C you need to (should be between 0 and 100 atoms per structure). Default value is 40"/>
        <param name="H_max_value" label="[1]H atom max number " type="integer" value="200" min="0" max="200" help="The maximum of H you need to (should be between 0 and 200 atoms per structure). Default value is 200"/>
        <param name="N_max_value" label="[15]N atom max number " type="integer" value="40" min="0" max="100" help="The maximum of N you need to (should be between 0 and 100 atoms per structure). Default value is 40"/>
        <param name="O_max_value" label="[16]O atom max number " type="integer" value="70" min="0" max="100" help="The maximum of O you need to (should be between 0 and 100 atoms per structure). Default value is 70"/>
        <param name="P_max_value" label="[31]P atom max number " type="integer" value="10" min="0" max="100" help="The maximum of P you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
        <param name="S_max_value" label="[32]S atom max number " type="integer" value="10" min="0" max="100" help="The maximum of S you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
        <param name="F_max_value" label="[19]F atom max number " type="integer" value="10" min="0" max="100" help="The maximum of F you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
        <param name="Cl_max_value" label="[35]Cl atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Cl you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
        <param name="K_max_value" label="[13]K atom max number " type="integer" value="10" min="0" max="100" help="The maximum of K you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
        <param name="Br_max_value" label="[80]Br atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Br you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
        <param name="Na_max_value" label="[23]Na atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Na you need to (should be between 0 and 40 atoms per structure). Default value is 10"/>
      </when>
      <when value="NO">
      </when>
    </conditional>
    <param name="verbose" type="select" label="Verbose level" display="radio" help="">
        <option value="1" selected="true">Low</option>
        <option value="3" >High</option>
    </param>
  </inputs>
  <outputs>
    <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/>
    <data name="hr2ResView" format="html" label="${tool.name}_VIEW"/>
  </outputs>
  
  <tests>
  	<test>
  		<param name="choice" value="NO"/>
  		<param name="masse" value="175.125"/>
  		<param name="tol" value="1.0"/>
  		<param name="mode" value="negative"/>
  		<param name="qtCharge" value="1"/>
  		<param name="atomes_basic" value="C,O,N,H"/>
  		<param name="regleOr" value="NO"/>
  		<param name="verbose" value="3"/>
  		<output name="variableMetadata" file="out1.tabular"/>
    </test>
    <test>
  		<param name="choice" value="NO"/>
  		<param name="masse" value="88.052"/>
  		<param name="tol" value="1.0"/>
  		<param name="mode" value="neutral"/>
  		<param name="qtCharge" value="1"/>
  		<param name="atomes_basic" value="C,O,H"/>
  		<param name="regleOr" value="NO"/>
  		<param name="verbose" value="3"/>
  		<output name="variableMetadata" file="out2.tabular"/>
    </test>
    <test>
  		<param name="choice" value="NO"/>
  		<param name="masse" value="427.019898895"/>
  		<param name="tol" value="1.0"/>
  		<param name="mode" value="neutral"/>
  		<param name="qtCharge" value="1"/>
  		<param name="atomes_basic" value="C,O,N,H,P"/>
  		<param name="atomes_sup" value="S"/>
  		<param name="S_max_value" value="40"/>
  		<param name="regleOr" value="NO"/>
  		<param name="verbose" value="3"/>
  		<output name="variableMetadata" file="out3.tabular"/>
    </test>
  </tests>
  
  <help><![CDATA[

.. class:: infomark

**Authors**
  | HR2 original program and its documentation are Copyright (c) 1992-2005 by Joerg Hau under GNU General Public License ("GPL")

.. class:: infomark

**Wrapping**
  | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and Perl wrapper)
  | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface, conda dependancies and Perl wrapper)

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

.. class:: infomark

**Please cite** If you use this tool, please cite
 | Tobias Kind and Oliver Fiehn. (2007). "Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry." BMC Bioinformatics p8:105 http://www.ncbi.nlm.nih.gov/pubmed/17389044
 | HR2 original program and its documentation are under GNU General Public License ("GPL") : GPL is a"contaminating" license. http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software


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

==============
HR2 formula
==============

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

 | Find a formula for the masses
 | only molecules with carbon (C) will be search


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


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




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

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

File variableMetadata must have at least the 2 following columns : 
  * Id : column to identify masses in the csv/tsv input file
  * Masses : column with all the masses in the csv/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 ; Column of Id ; Number of header ; Column of masses** are visible
  | NO : parameter **Mass of the molecule** is visible
  |


If 'use file'='YES'

Column of Id
  | Specify the column number for the id in the csv/tsv input file
  |

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

Column of masses
  | Specify the column number for the mass in the csv/tsv input file
  |

If 'use file'='NO'

Mass (MZ) 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 :

Delta
  | Tolerance of the gap in the mass
  | It should be between 0 and 9.0 mmu

Ionization
  | Type of ionization of the molecule : *positif, negatif, neutral*
  | Use neutral if query doesn't be a [M+H] or [M-H] ion
  | HR2 knows only the weight of uncharged molecules
  | so we made ​​a correction to the masses of the value of a proton before the search
  | if the masses are those from a spectrometry in positive or negatif mode.
  | **neutral** : will do a search on the mass unchanged.

Initial charge
  | Use 0 if the molecule is not basically charged

Exclude some basic atom(s)
  List of atoms that can be exclude to the molecule : *C, N, O, H, P*

Golden rules
  | There are 7 golden rules
  | Some are too stringent, especially for small molecules
  | Use 'yes' if you want more empirical formulas

Add some optionnal atom(s)
  List of atoms that can be searched in addition to the molecule : *S, F, Cl, K, Br, Na, 13C*

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

Two types of files
  | hr2_VIEW.HTML : for viewing result via HTML.
  | hr2_TSV.tabular : for linking with others modules.
  | an excel-like output will be available. 
  
---------------------------------------------------


---------------
Working example
---------------


.. class:: warningmark

Refer to the corresponding "W4M HowTo" in http://workflow4metabolomics.org/howto section
 | Format Data For Postprocessing
 | Perform LCMS Annotations

.. class:: warningmark

And their "W4M courses 2018":
 | Using Galaxy4Metabolomics - W4M table format for Galaxy
 | Les banques d'annotation - Annotation

  ]]></help>
  <citations>
    <citation type="doi">10.1186/1471-2105-8-105</citation>
  </citations>
</tool>