annotate ms_data_converter.xml @ 1:a36e9f847308 default tip

Fixes for running on Windows via pulsar

<tool id="ms_data_converter" name="MS Data Converter" version="1.3.0">
  <!-- BEGIN_VERSION_DEFAULT -->
  <description>for WIFF format using AB SCIEX MS Data Converter</description>
  <!-- END_VERSION_DEFAULT -->
  <!--
  <requirements>
    <requirement type="package" version="1.3beta">ab_sciex_ms_data_converter</requirement>
  </requirements>
-->
  <command interpreter="python">
    #import re
    #import os.path
    #set $ext = $input.ext
    ms_data_converter.py
    #set basename = 'absciex'
    #if hasattr($input, 'display_name')
        #set basename = $re.sub('\W','_',$input.display_name)
    #end if
    --input="${input.extra_files_path}/wiff"
    --input_name="${basename}.wiff"
    #### The os.path.exist did not work on Windows
    ## #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_scan')):
      --implicit="${input.extra_files_path}/wiff_scan"
      --input="${input.extra_files_path}/wiff_scan"
      --input_name="${basename}.wiff.scan"
    ## #end if
    #### The os.path.exist did not work on Windows
    ## #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_mtd')):
      --implicit="${input.extra_files_path}/wiff_mtd"
      --input="${input.extra_files_path}/wiff_mtd"
      --input_name="${basename}.wiff.mtd"
    ## #end if
    --output=${output}
    ## BEGIN_VERSION_DEFAULT
    --fromextension=$ext
    --content_type=$content_type
    ## END_VERSION_DEFAULT
    --toextension=${result.output_format}
    #if $result.output_format == "mzML"
    --zlib=${result.zlib}
    --binaryencoding=${result.precision}
    --index=${result.index}
    #end if
    --debug
  </command>

  <inputs>

    <!-- BEGIN_VERSION_DEFAULT -->
    <param format="wiff" name="input" type="data" label="Input wiff"/>
    <!-- END_VERSION_DEFAULT -->
    <conditional name="result">
        <param name="output_format" type="select" label="Output Format">
            <option value="mzML">mzML</option>
            <option value="mgf">mgf</option>
        </param>
        <when value="mzML">
            <param type="boolean" name="index" truevalue="true" falsevalue="false" checked="true" label="Index the mzML output"/>
            <param type="boolean" name="zlib" truevalue="true" falsevalue="false" checked="true" label="Binary zlib array compression"/>
            <param type="select" name="precision" label="Precision">
                <option value="32">32</option>
                <option value="64" selected="true">64</option>
            </param>
        </when>
        <when value="mgf"/>
    </conditional>
    <param name="content_type" type="select" label="Output Content Type">
      <option value="profile">profile</option>
      <option value="centroid">centroid</option>
      <option value="proteinpilot">proteinpilot</option>
    </param>
  </inputs>
  <outputs>
    <data format="mzml" name="output">
      <change_format>
        <when input="output_format" value="mgf" format="mgf" />
      </change_format>
    </data>
  </outputs>
  <help>
**What it does**

AB SCIEX MS Data Converter to convert mass spectral data from any AB SCIEX instrument into open data formats. Data can be converted into two different formats - mzML or mgf. You can also control what kind of information is written. You can choose to get an exact translation of what the instrument recorded or choose to convert to a processed version, reducing the data down to peak lists.

http://www.absciex.com/Documents/Downloads/Software/ABSCIEX-MS%20Data-Converter-User-Guide.pdf

------

**Citation**

If you use this tool in Galaxy, please cite Chilton J, et al. https://github.com/galaxyproteomics/

  </help>
</tool>