<tool id="mzxmlshaper" name="Mz(X)ML Shaper" version="1.0.0+galaxy0" profile="21.01">
  <description>
    conversion into XCMS-supported mz(X)ML file formats
  </description>
  <requirements>
    <requirement type="package" version="4.3.3">r-base</requirement>
    <requirement type="package" version="0.42.0">bioconductor-msdata</requirement>
    <requirement type="package" version="2.36.0">bioconductor-mzr</requirement>
    <requirement type="package" version="1.0.0">r-w4mrutils</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
    Rscript '$__tool_directory__/mzXMLShaper.R'
      inputfilename '$infile'
      outputfileformat '$outformat'
      #if str($outformat) == 'mzml':
        outputfilename '$mzml_file'
      #elif str($outformat) == 'mzXml':
        outputfilename '$mzXml_file'
      #end if
  ]]></command>
  <inputs>
    <param name="infile" type="data" format="mzml,mzxml,netcdf" label="File(s) to convert" help="file or collection"/>
    <param name="outformat" type="select" label="Desired output format">
      <option value="mzml">mzML</option>
      <option value="mzXml">mzXML</option>
    </param>
  </inputs>
  <outputs>
    <data format="mzml" label="${infile.name}_converted.mzml" name="mzml_file">
      <filter>outformat=="mzml"</filter>
    </data>
    <data format="mzxml" label="${infile.name}_converted.mzxml" name="mzXml_file">
      <filter>outformat=="mzXml"</filter>
    </data>
  </outputs>
  <tests>
    <test expect_num_outputs="1">
      <param name="infile" value="original_data/ko16.CDF"/>
      <param name="outformat" value="mzml"/>
      <output name="mzml_file" file="conversion_result_cdf_to_mzml.mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="infile" value="original_data/ko16.CDF"/>
      <param name="outformat" value="mzXml"/>
      <output name="mzXml_file" file="conversion_result_cdf_to_mzxml.mzxml"/>
    </test>
    <test expect_num_outputs="1">
      <param name="infile" value="original_data/ko16.mzXml"/>
      <param name="outformat" value="mzml"/>
      <output name="mzml_file" file="conversion_result_mzxml_to_mzml.mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="infile" value="original_data/ko16.mzXml"/>
      <param name="outformat" value="mzXml"/>
      <output name="mzXml_file" file="conversion_result_mzxml_to_mzxml.mzxml"/>
    </test>
    <test expect_num_outputs="1">
      <param name="infile" value="original_data/ko16.mzml"/>
      <param name="outformat" value="mzml"/>
      <output name="mzml_file" file="conversion_result_mzml_to_mzml.mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="infile" value="original_data/ko16.mzml"/>
      <param name="outformat" value="mzXml"/>
      <output name="mzXml_file" file="conversion_result_mzml_to_mzxml.mzxml"/>
    </test>
  </tests>
  <help><![CDATA[
.. class:: infomark

**Credits**
  | **Original tool wrapping:** Quentin Ruin - INRAE - MetaboHUB
  | **Tool maintainer:** Mélanie Pétéra - INRAE - MetaboHUB

.. class:: infomark

**Help and support:** https://community.france-bioinformatique.fr/c/workflow4metabolomics/10

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

******************
Mz(X)ML Shaper
******************
===========
DESCRIPTION
===========

This tool unables the user to convert any mass spectrometry file from netCDF (.cdf), .mzml or .mzxml format to "Pwiz-style" .mzml or .mzXml, as these are more often supported by the latest software. Files must be standard MS format (see Note below).
It is based on the R package mzR. This package (https://github.com/sneumann/mzR/) allows the user to access, read and copy the content of common MS file formats such as netCDF, mzML and mzXML. The output copy can be made in a different format, thus converting the file.
For more information about this package, see the related documentation (https://bioconductor.org/packages/release/bioc/html/mzR.html)

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

==========================
ALIGNMENT WITH OTHER TOOLS
==========================

-----------
INPUT FILES
-----------

Open format MS files (.netCDF, .mzML, .mzXML)

------------
OUTPUT FILES
------------

A file (or collection of files) converted in mzML or mzXML with the same name as the input file (except for the extension)

----------------------------
EXAMPLE OF WORKFLOW POSITION
----------------------------

Used as first step in any workflow supporting mzML or mzXML formats just before ReadMSData. 

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

===============
TOOL PARAMETERS
===============

- Desired output format: mzML or MZXML 

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

==================
OUTPUT DESCRIPTION
==================

Standardized MzML or mzXML files (depending on the user's configuration of the tool) 

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

==============
EXAMPLE OF USE
==============

.netCDF file upload -> Mz(X)MLShaper -> ReadMSData -> any workflow

------------
KNOWN ISSUES
------------

MzR does not read Bruker's DataAnalysis mzML or mzXML files, as they are not "standard" or "Pwiz-style" files (August 2024). This might also be the case for other constructor-converted mzML/mzXML, in that case an "unsupported file format" error will happen. However, this tool is functional for ProteoWizard's MSConvert mzML/mzXML files.
    
  ]]>
  </help>
  <citations>
    <citation type="doi">10.18129/B9.bioc.mzR</citation>
  </citations>
  </tool>