comparison msconvert.xml @ 9:dd4ba10d0c45 draft

planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6

8:d2c61663e33c

  <requirements>
    <requirement type="package" version="3_0_4388">proteowizard</requirement>
  </requirements>
-->
  <command interpreter="python">
    #set $ext = $input.ext
    msconvert_wrapper.py
    --input=${input}
    #if hasattr($input, 'display_name')
    --input_name='${input.display_name}'
    #end if
    --output=${output}
    ## BEGIN_VERSION_DEFAULT
    --fromextension=$ext
    ## END_VERSION_DEFAULT

      <param name="input_type" type="select" label="Input Type">
        <option value="mzml">mzML</option>
        <option value="mzxml">mzXML</option>
        <option value="mgf">mgf</option>
        <option value="ms2">ms2</option>
      </param>
      <when value="mzml">
        <param format="mzml" name="input" type="data" label="Input mzML"/>
      </when>
      <when value="mzxml">

      <when value="mgf">
        <param format="mgf" name="input" type="data" label="Input mgf"/>
      </when>
      <when value="ms2">
        <param format="ms2" name="input" type="data" label="Input ms2"/>
      </when>
    </conditional>
    <!-- END_VERSION_DEFAULT -->
    <param name="output_type" type="select" label="Output Type">
      <option value="mzML">mzML (indexed)</option>

    </conditional>


  </inputs>
  <outputs>
    <data format="mzml" name="output">
      <change_format>
        <when input="output_type" value="mzXML" format="mzxml" />
        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
        <when input="output_type" value="ms2" format="ms2" />
        <when input="output_type" value="mgf" format="mgf" />

9:dd4ba10d0c45

  <requirements>
    <requirement type="package" version="3_0_4388">proteowizard</requirement>
  </requirements>
-->
  <command interpreter="python">
    #import re
    #set $ext = $input.ext
    msconvert_wrapper.py
    #if $type.input_type == 'wiff':
      #set basename = 'absciex'
      #if hasattr($input, 'display_name')
        #set basename = $re.sub('\W','_',$input.display_name)
      #end if
      --input=${input.extra_files_path}/wiff
      --input_name='${basename}.wiff
      --implicit=${input.extra_files_path}/wiff_scan
      --input=${input.extra_files_path}/wiff_scan
      --input_name='${basename}.wiff.scan
    #else
      --input=${input}
      #if hasattr($input, 'display_name')
      --input_name='${input.display_name}'
      #end if
    #end if
    --output=${output}
    ## BEGIN_VERSION_DEFAULT
    --fromextension=$ext
    ## END_VERSION_DEFAULT

      <param name="input_type" type="select" label="Input Type">
        <option value="mzml">mzML</option>
        <option value="mzxml">mzXML</option>
        <option value="mgf">mgf</option>
        <option value="ms2">ms2</option>
        <option value="wiff">wiff</option>
      </param>
      <when value="mzml">
        <param format="mzml" name="input" type="data" label="Input mzML"/>
      </when>
      <when value="mzxml">

      <when value="mgf">
        <param format="mgf" name="input" type="data" label="Input mgf"/>
      </when>
      <when value="ms2">
        <param format="ms2" name="input" type="data" label="Input ms2"/>
      </when>
      <when value="wiff">
        <param format="wiff" name="input" type="data" label="Input wiff"/>
      </when>
    </conditional>
    <!-- END_VERSION_DEFAULT -->
    <param name="output_type" type="select" label="Output Type">
      <option value="mzML">mzML (indexed)</option>

    </conditional>


  </inputs>
  <outputs>
    <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" >
      <change_format>
        <when input="output_type" value="mzXML" format="mzxml" />
        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
        <when input="output_type" value="ms2" format="ms2" />
        <when input="output_type" value="mgf" format="mgf" />