<tool id="idconvert" name="idconvert" version="@VERSION@.0">
    <description>Convert mass spectrometry identification files</description>
    <requirements>
      <requirement type="package" version="3.0.9992">proteowizard</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <regex match="Error"
           source="both"
           level="fatal"
           description="Error" />
    </stdio>
    <command>
<![CDATA[
#import os.path
#set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
ln -s '$from.input' '$input_name' &&
idconvert '$input_name'
#if str($to_format) == 'pep.xml':
--pepXML
#elif str($to_format) == 'text':
--text
#end if
--outdir 'outdir'
&& cp outdir/* '$output'
]]>
    </command>
    <inputs> 
        <conditional name="from">
            <param name="from_format" type="select" label="Convert from">
                <option value="mzid">mzIdentML (mzid)</option>
                <option value="pepxml">pepXML (pepxml)</option>
                <option value="protxml">protXML (protxml)</option>
            </param>
            <when value="mzid">
                <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
            </when>
            <when value="protxml">
                <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
                <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" />
            </when>
            <when value="pepxml">
                <param name="input" type="data" format="pepxml" label="MS Identification" />
            </when>
        </conditional>
        <param name="to_format" type="select" label="Convert to">
            <option value="mzid">mzIdentML (mzid)</option>
            <option value="pep.xml">pepXML (pepxml)</option>
            <option value="text">text</option>
        </param>
    </inputs>
    <outputs>
        <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
            <change_format>
                <when input="to_format" value="pep.xml" format="pepxml" />
                <when input="to_format" value="text" format="txt" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="Rpal_01.pepXML" />
            <param name="from_format" value="pepxml" />
            <param name="to_format" value="mzid" />
            <output name="output">
                <assert_contents>
                    <has_text text="MzIdentML" />
                    <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="Rpal_01.mzid" />
            <param name="from_format" value="mzid" />
            <param name="to_format" value="pep.xml" />
            <output name="output">
                <assert_contents>
                    <has_text text="msms_pipeline_analysis" />
                    <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
idconvert [options] [filemasks]
Convert mass spec identification file formats.

Return value: # of failed files.

Options:
  -f [ --filelist ] arg    : specify text file containing filenames
  -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.]
  -c [ --config ] arg      : configuration file (optionName=value)
  -e [ --ext ] arg         : set extension for output files [mzid|pepXML|txt]
  --mzIdentML              : write mzIdentML format [default]
  --pepXML                 : write pepXML format
  --text                   : write hierarchical text format
  -v [ --verbose ]         : display detailed progress information
Examples:

# convert sequest.pepXML to sequest.mzid
idconvert sequest.pepXML

# convert sequest.protXML to sequest.mzid
# Also reads any pepXML file referenced in the 
# protXML file if available.  If the protXML 
# file has been moved from its original location, 
# the pepXML will still be found if it has also 
# been moved to the same position relative to the 
# protXML file. This relative position is determined 
# by reading the protXML protein_summary:summary_xml 
# and protein_summary_header:source_files values.
idconvert sequest.protXML

# convert mascot.mzid to mascot.pepXML
idconvert mascot.mzid --pepXML

]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btn323</citation>
    </citations>
</tool>