annotate vkmz.xml @ 7:b0ce669ce794 draft

planemo upload for repository https://github.com/HegemanLab/VKMZ commit 722cd42705f87f2dc11aa6984ae0836ad4ca41a6-dirty

<tool id="vkmz" name="vkmz" version="1.4dev1">

  <description>Metabolomics formula prediction and van Krevelen diagram generation</description>
  
  <requirements>
    <requirement type="package" version="3.6">python</requirement>
    <requirement type="package" version="v1.4dev1">vkmz</requirement>
  </requirements>
  
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>

  <command detect_errors="aggressive"><![CDATA[
    vkmz
    #if str( $mode.mode_selector ) == "w4m":
      xcms
      --data-matrix $mode.datamatrix
      --sample-metadata $mode.samplemetadata
      --variable-metadata $mode.variablemetadata
    #elif str( $mode.mode_selector ) == "tabular":
      tabular
      --input $mode.input
    #end if
    --error $prediction.error
    --database $prediction.database_type.database
    --output vkmz
    #if $advanced_input.polarity == "negative":
      --polarity negative
    #else if $advanced_input.polarity == "positive":
      --polarity positive
    #end if
    #if $advanced_input.impute_charge == "True":
      --impute_charge
    #end if
    #if $advanced_input.neutral == "True":
      --neutral
    #end if
    #if $advanced_input.alternate == "True":
      --alternate
    #end if
    #if $advanced_output.json == "True":
      --json
    #end if
    #if $advanced_output.sql == "True":
      --sql
    #end if
  ]]></command>

  <inputs>
    <conditional name="mode">
      <param name="mode_selector" type="select" label="Input Data">
        <option value="w4m">w4m</option>
        <option value="tabular">tabular</option>
      </param>
      <when value="w4m">
        <param name="datamatrix" label="W4M-XCMS Data Matrix" type="data" format="tabular" help="Select W4M-XCMS data matrix" />
        <param name="samplemetadata" label="W4M-XCMS Sample Metadata" type="data" format="tabular" help="Select W4M-XCMS sample metadata" />
        <param name="variablemetadata" label="W4M-XCMS Variable Metadata" type="data" format="tabular" help="Select W4M-XCMS variable metadata" />
      </when>
      <when value="tabular">
        <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="false">
      <param name="polarity" label="Override polarity" type="select" help="Force the polarity of all samples">
        <option value="NA">No override</option>
        <option value="negative">Negative</option>
        <option value="positive">Positive</option>
      </param>
      <param name="neutral" label="Disable polarity based mass adjustment" type="boolean" truevalue="True" help="Use this option if data contains neutral masses." />
      <param name="alternate" label="Keep feature's with more than one prediction" type="boolean" truevalue="False" help="Keeping features with multiple predictions raises the false discovery rate." />
      <param name="impute_charge" label="Impute Charge" type="boolean" truevalue="True" help="If impute data in annotated with charge information, features with no (null) charge valeus are removed. Setting Impute Charge to True imputes a charge for all of these features instead." />
    </section>
    <section name="prediction" title="Prediction Options" expanded="true">
      <param name="error" label="Mass Error (PPM)" type="float" value="10.0" min="0" help="Set according to expected 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>
          <option value="custom">Custom</option>
        </param>
	<when value="heuristic">
          <param name="database" label="Database" type="select" help="Select heuriestically generated database">
            <option value="databases/bmrb-light.tsv">Monoisotopic</option>
            <option value="databases/bmrb-heavy_carbon.tsv">C13 Labeled</option>
            <option value="databases/bmrb-heavy_nitrogen.tsv">N15 Labeled</option>
            <option value="databases/bmrb-heavy.tsv">C13 and C15 Labeled</option>
          </param>
        </when>
        <when value="custom">
          <param name="database" label="Database" type="data" format="tabular" help="Select a custom tabular database" />
        </when>
      </conditional>
    </section>
    <section name="advanced_output" title="Advanced Output Options" expanded="false">
      <param name="json" label="JSON" type="boolean" truevalue="False" help="Save results to JSON." />
      <param name="sql" label="SQL" type="boolean" truevalue="False" help="Save results to sqlite." />
    </section>
  </inputs>
  <outputs>
    <data format="tabular" name="output_tabular" from_work_dir="vkmz.tabular" label="${tool.name}_${mode.mode_selector}_tabular" />
    <data format="html" name="output_html" from_work_dir="vkmz.html" label="${tool.name}_${mode.mode_selector}_html" />
    <data format="json" name="output_json" from_work_dir="vkmz.json" label="${tool.name}_${mode.mode_selector}_json" />
    <data format="sqlite" name="output_sqlite" from_work_dir="vkmz.db" label="${tool.name}_${mode.mode_selector}_sqlite" />
  </outputs>

  <tests>
    <test>
      <conditional name="mode">
        <param name="mode_selector" value="w4m" />
        <param name="datamatrix" value="datamatrix.tabular" />
        <param name="samplemetadata" value="sampleMetadata.tabular" />
        <param name="variablemetadata" value="variableMetadata.tabular" />
      </conditional>
      <param name="error" value="10" />
      <param name="database" value="databases/bmrb-light.tsv" />
      <output name="output_tabular">
        <assert_contents>
      	  <has_text text="C6H7NO2" />
        </assert_contents>
      </output>
    </test>
  </tests>

  <help><![CDATA[
============
VKMZ 1.4dev1
============

VKMZ is a metabolomics prediction and vizualization tool which creates van Krevelen diagrams from mass spectrometry data. A van Krevelen diagram (VKD) plots a molecule on a scatterplot by the molecules oxygen to carbon ratio (O:C) against it's hydrogen to carbon ratio (H:C). Classes of metabolites cluster together on a VKD [0]. Plotting a complex mixture of metabolites on a VKD briefly conveys untargeted metabolomics data.

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

**Input Data**

VKMZ is designed to use W4M-XCMS [1] or tabular data as input.

*W4M* mode requires three files which W4M's XCMS wrapper 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*. Set this if input does not contain the correct polarity information. This option should not be used if data contains both positive and negative polarity.

*Neutral* disable mass adjustment of features in case nominal exact mass information is present instead of m/z.

**Prediction Options**

For each feature VKMZ attempts to predict a molecular formula by comparing the feature's uncharged mass to a database of known formula masses. A prediction is made when a known mass is within a mass error of observed, uncharged, mass. VKMZ finds all predictions for an observed mass within a specified 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.
 
*Mass error* sets the mass error in parts per million. Mass error will be specific to your mass spectrometer, calibration and other methods. Mass error can be approximated by running similar methods with targeted standards with a range in mass.

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

**Tabular Output**

Tabular output contians the columns: sample_id, polarity, mz, rt (retentnion time), intensity, predictions (list of list-elements which contains: predicted mz, predicted formula, and predicted delta), hc (hydrogen to carbon ratio), oc, nc.

**HTML Output**

The HTML web page is an interactive van Krevelen diagram for exploring data.

Predicted features are plotted as circle symbols.

*Min Size* and *Max Size* sets the minimal and maximum area of symbols (absolute scaling).

The *Sizer* dropdown sets the algorithm to size each symbol.

  * *Uniform* sets the symbols of all features to the *Max Size*.
  * *Relative Intensity* sets the symbol size of each feature by the feature's intensity divided by the maxium intensity in the dataset mutiplied by the *Maxium Symbol Size*.
  * *Relative Log Intensity* sets the symbol size of each feature by the feature's log intensity divided by the maxium log intensity in the dataset mutiplied by the *Maxium Symbol Size*.

*Threshold* is a slider which removes low-intensity features. The slider exponentially scales.

  * Setting the slider to 50% removes features with intensities lower than 25% of the maximum inensity.
  * Setting the slider to 75% removes features with intensities lower than 50% of the maximum inensity.

*x-axis* and *y-axis* allow setting axis to alternate elemental ratios.

*Opacity* sets the opacity of feature symbols.

*Visible Samples* sets the visibility of features from given sample IDs. Checked samples are visible. By default all samples are visible.
 
  ]]></help>

  <citations>
    <citation type="doi">10.1007/s11306-018-1343-y</citation>
    <citation type="doi">10.1021/ac051437y</citation>
    <citation type="doi">10.1021/ac070346t</citation>
  </citations>

</tool>