comparison vkmz.xml @ 2:d4a9e43aca74 draft

planemo upload for repository https://github.com/HegemanLab/VKMZ commit e0957db19910fc23456bbd8ac59d61f77ffc6dc5-dirty

1:b02af8eb8e6e

      --variable-metadata $mode.variablemetadata
    #elif str( $mode.mode_selector ) == "tsv":
      tsv
      --input $mode.input
    #end if
    #if $no_adjustment=="True":
      --no-adjustment
    #end if
    --output vkmz
    --error $prediction.error
    --database $prediction.database_type.database

    --directory $__tool_directory__/
  ]]></command>

  <inputs>
    <conditional name="mode">
      <param name="mode_selector" type="select" label="Input data type">
        <option value="xcms">xcms</option>
        <option value="tsv">tsv</option>
      </param>
      <when value="xcms">
        <param name="datamatrix" label="XCMS Data Matrix" type="data" format="tabular" help="Select XCMS data matrix" />

      </when>
      <when value="tsv">
        <param name="input" label="Tabular input" type="data" format="tabular" help="Select tabular data" />
      </when>
    </conditional>
    <param name="no_adjustment" label="Turn off mass adjustment" type="boolean" truevalue="True" help="Turn off polarity based mass adjustment. No adjustment should always be selected if reprocessing data generated by VKMZ." />
    <section name="prediction" title="Prediction Options" expanded="true">
      <param name="error" label="Mass Error (PPM)" type="float" value="3.0" min="0" help="Set according to mass spectrometer's mass error in parts-per-million" />
      <conditional name="database_type">
        <param name="database_type_selector" type="select" label="Database Type">
          <option value="heuristic">Heuristically Generated</option>

=============
Documentation
=============

**Input Modes**

VKMZ is designed to use XCMS [1] data as input. Tabular data can also be used as input.

*XCMS* mode requires three files which XCMS generates: the data matrix, sample metadata, and variable metadata files.

*Tabular* mode requires a tab delimited file with the first five columns being: sample_id, polarity, mz, retention_time, and intensity.

**Mass adjustment**

To calculate a features nominal mass VKMZ adjusts masses by removing or adding the mass of a proton based on polarity.

Mass adjustment should be turned off if using nominal mass data. VKMZ tabular output contains nominal masses.

**Prediction Options**

For each feature in the data VKMZ attempts to predict a molecular formula by comparing the feature's mass to a database of known formula masses. A prediction is made when a known mass is within a mass error of the observed mass. VKMZ finds all predictions for an observed mass within the mass error. The prediction with the lowest delta, absolute difference between observed and known mass, is plotted. Features without predictions are discarded. Using low resolution data may result in finding too many predictions per feature to be useful, especially for large mass metabolites.
 
Set the mass error option to the mass error, in parts per million, of the mass spectrometer which collected the initial data. 

Heuristically generated databases for unlabeled and labeled formulas are included with VKMZ [2]. Custom database can also be set.

**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>

2:d4a9e43aca74

      --variable-metadata $mode.variablemetadata
    #elif str( $mode.mode_selector ) == "tsv":
      tsv
      --input $mode.input
    #end if
    #if $advanced_input.polarity=="negative":
      --polarity negative
    #else if $advanced_input.polarity=="positive":
      --polarity positive
    #end if
    #if $advanced_input.no_adjustment=="True":
      --no-adjustment
    #end if
    --output vkmz
    --error $prediction.error
    --database $prediction.database_type.database

    --directory $__tool_directory__/
  ]]></command>

  <inputs>
    <conditional name="mode">
      <param name="mode_selector" type="select" label="Input Data">
        <option value="xcms">xcms</option>
        <option value="tsv">tsv</option>
      </param>
      <when value="xcms">
        <param name="datamatrix" label="XCMS Data Matrix" type="data" format="tabular" help="Select XCMS data matrix" />

      </when>
      <when value="tsv">
        <param name="input" label="Tabular input" type="data" format="tabular" help="Select tabular data" />
      </when>
    </conditional>
    <section name="advanced_input" title="Advanced Input Options" expanded="fals:we">
      <param name="polarity" label="Override polarity" type="select" help="Set polarity for all samples ignoring input files">
        <option value="NA">No override</option>
        <option value="negative">Negative</option>
        <option value="positive">Positive</option>
      </param>
      <param name="no_adjustment" label="Disable polarity based mass adjustment" type="boolean" truevalue="True" help="Use this option if data contains neutral masses." />
    </section>
    <section name="prediction" title="Prediction Options" expanded="true">
      <param name="error" label="Mass Error (PPM)" type="float" value="3.0" min="0" help="Set according to mass spectrometer's mass error in parts-per-million" />
      <conditional name="database_type">
        <param name="database_type_selector" type="select" label="Database Type">
          <option value="heuristic">Heuristically Generated</option>

=============
Documentation
=============

**Input Data**

VKMZ is designed to use XCMS [1] data as input. Tabular data can also be used as input.

*XCMS* mode requires three files which XCMS generates: the data matrix, sample metadata, and variable metadata files.

*Tabular* mode requires a tab delimited file with the first five columns being: sample_id, polarity, mz, retention_time, and intensity.

**Advanced Input Options**

*Override polarity* allows users to set the polarity of all features to either positive or negative. This option should not be used if data contains both polarity types.

*Disable mass adjustment* prevents converting charged masses to neutral masses. If you are using neutral mass data this option should be used.

**Prediction Options**

For each feature in the data VKMZ attempts to predict a molecular formula by comparing the feature's mass to a database of known formula masses. A prediction is made when a known mass is within a mass error of the observed mass. VKMZ finds all predictions for an observed mass within the mass error. The prediction with the lowest delta, absolute difference between observed and known mass, is plotted. Features without predictions are discarded. Using low resolution data may result in finding too many predictions per feature to be useful, especially for large mass metabolites.
 
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>