annotate bank_inhouse.xml @ 1:52798007c6b2 draft default tip

Master branch Updating - - Fxx

<tool id="bank_inhouse" name="bank_inhouse" version="1.2.1">
  <description>
        search by accurate mass (and by Retention time) on a local bank
  </description>
  
  <requirements>
  	<requirement type="package" version="2.90">perl-json</requirement>
  	<requirement type="package" version="1.97">perl-text-csv</requirement>
  	<requirement type="package" version="6.15">perl-lwp-simple</requirement>
  	<requirement type="package" version="1.74">perl-uri</requirement>
  	<requirement type="package" version="1.19">perl-soap-lite</requirement>
  	<requirement type="package" version="2.97">perl-html-template</requirement>
  	<requirement type="package" version="0.428">perl-list-moreutils</requirement>
  	<requirement type="package" version="6.15">perl-libwww-perl</requirement>
  </requirements>
  <stdio>
      <exit_code range="1" level="fatal" />
  </stdio>
  
   <command><![CDATA[
      perl $__tool_directory__/bank_inhouse.pl
      
      #if str($input_type.choice) == "YES":
         -input "${input_type.variableMetadata_in}"
         #if str($input_type.header.header_choice) == "YES":
             -nbheader "${input_type.header.nbheader}"
         #end if
         
         -colmass "${input_type.colmass}"
         #if str($input_type.use_file_rt.rt_file_choice) == "YES":
             -colrt "${input_type.use_file_rt.colrt}"
             -rt_delta "${input_type.use_file_rt.rt_file_delta}"
         #end if
      #else:
         #if str($input_type.use_rt.rt_choice) == "YES":
             -rt "${input_type.use_rt.rt}"
             -rt_delta "${input_type.use_rt.rt_delta}"
         #end if
         -masse "${input_type.masse}"
      #end if
      
      -mz_delta "${mz_delta_type.mz_delta}"
      -mass_delta "${mz_delta_type.mass_delta}"

      #if str($bank_type.perso_bank) == "YES":
         -bank_in "${bank_type.bank_in}" -bank_name "${bank_type.bank_in.name}"
         -mzdb "${bank_type.mzdb}"
         #if str($bank_type.bank_rt.bank_rt_choice) == "YES":
             -rtdb "${bank_type.bank_rt.rtdb}"
         #end if
      #end if

      #if str($input_type.choice) == "YES":
          -outputTab "$variableMetadata_out"
          -outputXls "$bankInhouseResXls_filein"
          #if str($outfiles) == "YES":
            -outputFull "$variableMetadata_full_out"
          #end if
      #else:
          -outputXls "$bankInhouseResXls_manualin"
      #end if
      
      #if str($outfiles) == "YES":
        -outputJson "$Json"
      #end if
  ]]></command>
  
  <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="NO">NO</option>
          <option value="YES" selected="true">YES</option>
        </param>
        <when value="YES">
          <param name="variableMetadata_in" type="data" label="FILE OF MASSES (format: tabular)" help="Generally variable metadata file" format="tabular" />
          
          <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" 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>
          
          <conditional name="use_file_rt">
            <param name="rt_file_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Would you use retention time (RT)?" help="Do you have retention times in your bank? In your analyzed file? Would you use it?" />
            <when value="YES">
              <param name="colrt" label="Column of retention time (RT)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
              <param name="rt_file_delta" label="Delta of retention time (RT) (in minutes)" type="float" value="0.1" min="0" max="60" help="Default value is 0.1min"/>
            </when>
            <when value="NO"/>
          </conditional>
          
          <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
        </when>
        <when value="NO">
          <conditional name="use_rt">
            <param name="rt_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Would you use retention time (RT)?" help="Do you have retention times in your bank? Would you use it?" />
            <when value="YES">
              <param name="rt" label="retention time (RT) to submit" type="text" size="10" help="For a rt list, writes : rt1 rt2 rt3. Your values ​​must be separated by spaces. You should use dot (.) like decimal separator"/>
              <param name="rt_delta" label="Delta of retention time (RT) (in minutes)" type="float" value="0.1" min="0" max="60" help="Default value is 0.1min"/>
            </when>
            <when value="NO"/>
          </conditional>
          
          <param name="masse" type="text" label="Mass (MZ) to submit"  size="20" 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>
      
      <conditional name="mz_delta_type">
        <param name="mz_delta" label="Delta type" type="select"  display="radio" help="">
          <option value="Da">Da</option>
          <option value="ppm">ppm</option>
        </param>
        <when value="Da">
          <param name="mass_delta" label="Delta of mass (MZ) (in Dalton)" type="float" value="0.005" min="0" max="3000" help="Default value is 0.005 Da"/>
        </when>
        <when value="ppm">
          <param name="mass_delta" label="Delta of mass (MZ) (in ppm)" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/>
        </when>
      </conditional>
      
      <conditional name="bank_type">
         <param name="perso_bank" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="* Use personal data bank?" help="if 'NO' is selected an internal file will be used! It doesn't contain a retention time (RT)" />
         <when value="YES">
            <param name="bank_in" type="data" label="BANK FILE" help="" format="tabular" />
            <param name="mzdb" label="Column of masses (MZ) in Bank file" type="data_column" data_ref="bank_in" accept_default="true" />
            <conditional name="bank_rt">
              <param name="bank_rt_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Have you used the retention time (RT) for your input data?" help="Do you have retention times in your bank? In your analyzed data? Would you use it?" />
              <when value="YES">
                <param name="rtdb" label="Column of retention time (RT) in Bank file" type="data_column" data_ref="bank_in" accept_default="true" />
              </when>
              <when value="NO"/>
            </conditional>
         </when>
         <when value="NO"/>
    </conditional>
    <param name="outfiles" type="select" label="* Would you more output?" display="radio" help="if 'YES' is selected then 2 more files will be generate (JSON + variableMetadata and bank full column)">
        <option value="YES">YES</option>
        <option value="NO" selected="true">NO</option>
    </param>
  </inputs>
  
  <outputs>
    <data name="variableMetadata_out" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_TSV" >
      <filter>(input_type['choice'] == 'YES')</filter>
    </data>
    <data name="bankInhouseResXls_filein" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_XLS" >
      <filter>(input_type['choice'] == 'YES')</filter>
    </data>
    <data name="variableMetadata_full_out" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_full_TSV" >
      <filter>(input_type['choice'] == 'YES')</filter>
      <filter>(outfiles == 'YES')</filter>
    </data>
    <data name="bankInhouseResXls_manualin" format="tabular" label="${tool.name}_manual_XLS" >
      <filter>(input_type['choice'] == 'NO')</filter>
    </data>
    <data name="Json" format="vjson" label="${tool.name}_Json" >
      <filter>(outfiles == 'YES')</filter>
    </data>
    <!--<data name="View" format="html" label="${tool.name}_View" ></data>-->
  </outputs>
  
  <tests>
    <test>
      <param name="choice" value="NO"/>
      <param name="rt_choice" value="NO"/>
      <param name="masse" value="422.0849114 18.0105647 535.3181236 209.987659 98.952389"/>
      <param name="mz_delta" value="Da"/>
      <param name="mass_delta" value="0.005"/>
      <param name="perso_bank" value="NO"/>
      <param name="outfiles" value="NO"/>
      <output name="bankInhouseResXls_manualin" file="out_test1.tabular"/>
    </test>
    <test>
      <param name="choice" value="YES"/>
      <param name="variableMetadata_in" value="in_test2.tabular"/>
      <param name="header_choice" value="YES"/>
      <param name="nbheader" value="1"/>
      <param name="rt_file_choice" value="NO"/>
      <param name="colmass" value="2"/>
      <param name="mz_delta" value="Da"/>
      <param name="mass_delta" value="0.005"/>
      <param name="perso_bank" value="NO"/>
      <param name="outfiles" value="NO"/>
  
      <output name="variableMetadata_out" file="out_test2a.tabular"/>
      <output name="bankInhouseResXls_filein" file="out_test2b.tabular"/>
    </test>
    <!--
    <test>
      <param name="choice" value="YES"/>
      <param name="variableMetadata_in" value="in_test3.tabular"/>
      <param name="header_choice" value="YES"/>
      <param name="nbheader" value="1"/>
      <param name="rt_file_choice" value="NO"/>
      <param name="colmass" value="2"/>
      <param name="mz_delta" value="Da"/>
      <param name="mass_delta" value="0.005"/>
      <param name="perso_bank" value="NO"/>
      <param name="outfiles" value="NO"/>
  
      <output name="variableMetadata_out" file="out_test3a.tabular"/>
      <output name="bankInhouseResXls_filein" file="out_test3b.tabular"/>
    </test>
    <test>
      <param name="choice" value="YES"/>
      <param name="variableMetadata_in" value="in_test4.tabular"/>
      <param name="header_choice" value="YES"/>
      <param name="nbheader" value="1"/>
      <param name="rt_file_choice" value="YES"/>
      <param name="colrt" value="10"/>
      <param name="rt_file_delta" value="0.2"/>
      <param name="colmass" value="8"/>
      <param name="mz_delta" value="Da"/>
      <param name="mass_delta" value="0"/>
      <param name="perso_bank" value="YES"/>
      <param name="bank_in" value="in_test4.tabular"/>
      <param name="mzdb" value="8"/>
      <param name="bank_rt_choice" value="YES"/>
      <param name="rtdb" value="10"/>
      <param name="outfiles" value="YES"/>
  
      <output name="variableMetadata_out" file="out_test4a.tabular"/>
      <output name="bankInhouseResXls_filein" file="out_test4b.tabular"/>
      <output name="variableMetadata_full_out" file="out_test4c.tabular"/>
      <output name="Json" file="out_test4d.vjson"/>
    </test>-->
  </tests>
  
  <help><![CDATA[

.. class:: infomark

**Authors**
  | Jean-François Martin - PFEM ; INRA ; MetaboHUB (for original version in R)
  | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for adapted version and development of this Perl script and for xml interface and Perl wrapper)
  | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for actual dev and maintaining)

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


==============
bank_inhouse
==============

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

 | Search informations on a local bank with one or more mass(es), with or without retention time, in a file or entered manually


Keywords
========

Masses + rt to inhouse info


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


.. image:: bank_inhouse.png
        :width: 800


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


+-----------------------------+-----------+
| Parameter : num + label     |  Format   |
+=============================+===========+
| 1 : File of masses          |  tabular  |
+-----------------------------+-----------+
| 2 : personal data bank file |  tabular  |
+-----------------------------+-----------+

File of masses (Generally variable metadata file) must have at least the 2 following column : 
    | Id : column to identify masses in the tsv input file
    | Masses : column with all the masses in the tsv input file
    | RT : (optional) column with all the retention time in the tsv input file
    | 

personal data bank file must contain certain columns :
    | Masses (Mandatory) and RT (optional)
    | 

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

Would you use a file
    | Choose whether the masses are in a file or entered manually
    | YES (default) : parameters **File of masses ; Do you have a header ; Column of Id ; Column of masses** are visible
    | NO : parameter **Mass to submit** is visible
    |


If 'use file'='YES'

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 Id
    | Specify the column number for the id in the tsv input file
    |

Would you use retention time (RT)
    | YES (default) : parameter **Column of retention time (RT)** and **Delta of retention time (RT) (in minutes)** are visible
    | NO : Search will be made solely on the basis of the masses
    |

If 'Would you use retention time (RT)'='YES'

Column of retention time (RT)
    | Specify the column number for the retention time (RT) in the tsv input file
    |

Delta of retention time (RT) (in minutes)
    | Specify a delta to apply on  retention time - This value is a float.
    |

In all RT cases :

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


If 'use file'='NO'

Would you use retention time (RT)
    | YES (default) : parameter **retention time (RT) to submit** and **Delta of retention time (RT) (in minutes)** are visible
    | NO : Search will be made solely on the basis of the masses
    |

If 'Would you use retention time (RT)'='YES'

retention time (RT) to submit 
    | Specify a list of retention time to request
    | one or more retention time entered manually
    | For a RT list, writes : rt1 rt2 rt3
    | You must separate yours values with space
    | dot (.) is for float number
    |
Delta of retention time (RT) (in minutes)
    | Specify a delta to apply on  retention time - This value is a float.
    |

In all RT cases :

Mass 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 type 
    | Specify a delta type : "in Dalton" or "in ppm"
    |

Delta of mass ("in Dalton" or "in ppm" according to choice)
    | Specify a delta to apply on mass - This value is a float.
    |

Use personal data bank
    | YES : parameter **Bank file**, **Column of masses (MZ) in Bank file** and **Column of retention time (RT) in Bank file** (optional) are visible, the search will be made only on the information of the file
    | NO : a internal bank will be used
    |

If 'Use personal data bank'='YES'

Bank file
    | see "Input files" section above
    | Tabular file format, Generally variable metadata file
    | 

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

Have you used the retention time (RT) for your input data 
    | Answering same as for "Would you use retention time (RT)"
    | YES (default) : parameter **Column of retention time (RT) in Bank file** is visible
    | NO : Search will be made solely on the basis of the masses
    |

Column of retention time (RT) in Bank file
    | Specify the column number for the rt in the bank input file
    |


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

Two types of files (if you manually enter the masses both files are mingled):
    | bank_inhouse_(input.name)_TSV.tabular : for linking with others modules.
    | 
    | bank_inhouse_(input.name)_XLS.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 2018":
 | Using Galaxy4Metabolomics - W4M table format for Galaxy
 | Annotation Banks - Annotation  
	
	]]></help>
</tool>