comparison vkmz.xml @ 5:04079c34452a draft

planemo upload for repository https://github.com/HegemanLab/VKMZ commit 3e37abe007f126480b9b748ad5322755445ac95b-dirty

4:1c2fe3a17065

<tool id="VKMZ" name="VKMZ" version="1.1">

  <description>metabolomics formula prediction and van Krevelen diagram generation</description>
  
  <requirements>
    <requirement type="package" version="2.7">python</requirement>

      --no-adjustment
    #end if
    --output vkmz
    --error $prediction.error
    --database $prediction.database_type.database
    --size $diagram.size
    --size-algorithm $diagram.sizealgorithm
    --directory $__tool_directory__/
  ]]></command>

        </when>
        <when value="custom">
          <param name="database" label="Database" type="data" format="tabular" help="Select a custom tabular database" />
        </when>
      </conditional>
    </section>
    <section name="diagram" title="Diagram Options" expanded="true">
      <param name="size" label="Minimum Maker Size" type="integer" value="5" min="0" help="Set the base size of diagram's markers" />
      <param name="sizealgorithm" label="Marker Size Algorithm" type="select" help="Select algorithm to change marker sizes. 1.) Set all markers to the base size, 2.) Marker sizes are relative to feature's log intensity">
        <option value="0">Uniform</option>

 
Set *Mass error* to the mass error, in parts per million, of the mass spectrometer which collected the data. 

*Database* can be set to heuristically generated databases for unlabeled and labeled chemcials [2] or to a custom database.

**Diagram Options**

Predicted features are plotted as markers. The size of each marker is determined by the minimum marker size and a marker size algorithm. The marker size algorithms use minimum marker size as a variable. 
  ]]></help>

5:04079c34452a

<tool id="VKMZ" name="VKMZ" version="1.1.1">

  <description>metabolomics formula prediction and van Krevelen diagram generation</description>
  
  <requirements>
    <requirement type="package" version="2.7">python</requirement>

      --no-adjustment
    #end if
    --output vkmz
    --error $prediction.error
    --database $prediction.database_type.database
    #if $prediction.unique=="True":
      --unique
    #end if
    --size $diagram.size
    --size-algorithm $diagram.sizealgorithm
    --directory $__tool_directory__/
  ]]></command>

        </when>
        <when value="custom">
          <param name="database" label="Database" type="data" format="tabular" help="Select a custom tabular database" />
        </when>
      </conditional>
      <param name="unique" label="Unique matches" type="boolean" truevalue="True" help="Only output features with a single prediction" />
    </section>
    <section name="diagram" title="Diagram Options" expanded="true">
      <param name="size" label="Minimum Maker Size" type="integer" value="5" min="0" help="Set the base size of diagram's markers" />
      <param name="sizealgorithm" label="Marker Size Algorithm" type="select" help="Select algorithm to change marker sizes. 1.) Set all markers to the base size, 2.) Marker sizes are relative to feature's log intensity">
        <option value="0">Uniform</option>

 
Set *Mass error* to the mass error, in parts per million, of the mass spectrometer which collected the data. 

*Database* can be set to heuristically generated databases for unlabeled and labeled chemcials [2] or to a custom database.

*Unique matches* removes features from the output which have multiple predictions. Low mass molecules are less affected by this filter than high mass molecules.

**Diagram Options**

Predicted features are plotted as markers. The size of each marker is determined by the minimum marker size and a marker size algorithm. The marker size algorithms use minimum marker size as a variable. 
  ]]></help>