comparison msconvert3_raw.xml @ 5:08bb52273ae1

Bjoern: remove unused repository dependency, cleanups

4:001e77708ec9

<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.0">
  <!-- BEGIN_VERSION_RAW -->
  <description>Convert and filter a Thermo Finnigan RAW file</description>
  <!-- END_VERSION_RAW -->

  <command interpreter="python">
    #set $ext = $input.ext
    #if $ext.startswith("m:")
    #set $ext = $ext[len("m:"):]
    #end if

  <inputs>
    <!-- BEGIN_VERSION_RAW -->
    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/>
    <!-- END_VERSION_RAW -->

    <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is the standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)">
      <option value="mzML">mzML (indexed)</option>
      <option value="unindexed_mzML">mzML (unindexed)</option>
      <option value="mzXML">mzXML (indexed)</option>      
      <option value="unindexed_mzXML">mzXML (unindexed)</option>
      <option value="mgf">mgf</option>
      <option value="ms2">ms2</option>  
    </param>    
    <conditional name="filtering">
      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (also called as peaklist processing)" />
      <when value="false" />
      <when value="true">
        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
        <!-- BEGIN_VERSION_3 -->
        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />

        <when input="output_type" value="ms2" format="ms2" />
        <when input="output_type" value="mgf" format="mgf" />
      </change_format>
    </data>
  </outputs>

  <requirements>
    <requirement type="package">proteowizard</requirement>    
    <!-- BEGIN_VERSION_RAW -->
    <requirement type="platform">windows</requirement>
    <!-- END_VERSION_RAW -->    
  </requirements>

  <help>
**What it does**

Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.

You can view the original documentation here_.
    
.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html

**Recommended**

For X!tandem searches: Use mzml format generated from RAW file.

                                       RAW → mzml

For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter.

                                       RAW → mzml → MGF (ProteinPilot)

For MaxQuant searches: Use RAW file as an input.

For OMSSA : Use MGF format generated from mzml file using MGF formatter.

                                       RAW → mzml → MGF (Mascot)
------

**Citation**

For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`

5:08bb52273ae1

<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.1">
  <!-- BEGIN_VERSION_RAW -->
  <description>Convert and filter a Thermo Finnigan RAW file</description>
  <!-- END_VERSION_RAW -->
  <requirements>
    <requirement type="package">proteowizard</requirement>
    <!-- BEGIN_VERSION_RAW -->
    <requirement type="platform">windows</requirement>
    <!-- END_VERSION_RAW -->
  </requirements>
  <command interpreter="python">
    #set $ext = $input.ext
    #if $ext.startswith("m:")
    #set $ext = $ext[len("m:"):]
    #end if

  <inputs>
    <!-- BEGIN_VERSION_RAW -->
    <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/>
    <!-- END_VERSION_RAW -->

    <param name="output_type" type="select" label="Output Type">
      <option value="mzML">mzML (indexed)</option>
      <option value="unindexed_mzML">mzML (unindexed)</option>
      <option value="mzXML">mzXML (indexed)</option>      
      <option value="unindexed_mzXML">mzXML (unindexed)</option>
      <option value="mgf">mgf</option>
      <option value="ms2">ms2</option>  
    </param>    
    <conditional name="filtering">
      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
      <when value="false" />
      <when value="true">
        <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
        <!-- BEGIN_VERSION_3 -->
        <param type="boolean" name="precursor_refine" label="Refine Precursor?" />

        <when input="output_type" value="ms2" format="ms2" />
        <when input="output_type" value="mgf" format="mgf" />
      </change_format>
    </data>
  </outputs>
  <help>
**What it does**

Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.

You can view the original documentation here_.
    
.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html

------

**Citation**

For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`