<tool id="proteinpilot" version="0.2.1" name="ProteinPilot">
  <description></description>
  <!-- ESCAPE input and database name -->
  <configfiles>
    <configfile name="input_config">## Describe input groups
group:DEFAULT_GROUP
#for $input in $inputs:
name:${input.display_name}
path:${input}
#end for
</configfile>
  </configfiles>  
  <command interpreter="python">proteinpilot_wrapper.py 
    --input_config="$input_config"
    --database="${database}"
    --database_name="${database.display_name}"
    --output=$output
    --output_methods=$output_methods
    --sample_type="$sample_type"
    --quantitative=$quantitative
    --bias_correction=$bias_correction
    --background_correction=$background_correction
    --cys_alkylation="$cys_alkylation"
    --digestion="$digestion"
    --instrument="$instrument"
    --search_effort=$search_effort
    --pspep=$pspep
    #if $pspep
    --output_pspep_report=$output_pspep_report
    #end if
    --min_unused_protscore=$min_unused_protscore
    #if $factors.factors_use
    --special_factors="$factors.special_factors"
    #else
    --special_factors=""
    #end if 
    --search_foci="$search_foci"
  </command>
  <inputs>
    <param format="mgf" multiple="true" name="inputs" type="data" label="Peaklist (MGF)" help="" />
    <param type="select" name="sample_type" label="Sample Type">
      <option value="Identification">Identification</option>
      <option value="iTRAQ 4plex (Peptide Labeled)">iTRAQ 4plex (Peptide Labeled)</option>
      <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option>
      <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option>
      <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option>
      <option value="TMT6plex ID-only (Peptide Labeled)">TMT6plex ID-only (Peptide Labeled)</option>
      <option value="TMT6plex ID-only (Protein Labeled)">TMT6plex ID-only (Protein Labeled)</option>
      <option value="TMT2plex ID-only (Peptide Labeled)">TMT2plex ID-only (Peptide Labeled)</option>
      <option value="TMT ID-only (Peptide Labeled)">TMT ID-only (Peptide Labeled)</option>
      <option value="mTRAQ (Peptide Labeled - M00, M04)">mTRAQ (Peptide Labeled - M00, M04)</option>
      <option value="mTRAQ (Peptide Labeled - M00, M08)">mTRAQ (Peptide Labeled - M00, M08)</option>
      <option value="mTRAQ (Peptide Labeled - M04, M08)">mTRAQ (Peptide Labeled - M04, M08)</option>
      <option value="mTRAQ (Peptide Labeled - M00, M04, M08)">mTRAQ (Peptide Labeled - M00, M04, M08)</option>
      <option value="SILAC (Lys+6, Arg+6)">SILAC (Lys+6, Arg+6)</option>
      <option value="SILAC (Lys+4, Arg+10)">SILAC (Lys+4, Arg+10)</option>
      <option value="SILAC (Lys+6, Arg+10)">SILAC (Lys+6, Arg+10)</option>
      <option value="SILAC (Lys+8, Arg+10)">SILAC (Lys+8, Arg+10)</option>
      <option value="SILAC (Lys+8, Arg+10, Glu+6, Asp+5)">SILAC (Lys+8, Arg+10, Glu+6, Asp+5)</option>
      <!-- TODO: Add remaining SILAC options. -->
      <option value="RABA +0,+6 (Peptide Labeled)">RABA +0,+6 (Peptide Labeled)</option>
      <option value="Dimethyl +0,+4 (Peptide Labeled)">Dimethyl +0,+4 (Peptide Labeled)</option>
      <option value="Dimethyl +0,+6 (Peptide Labeled)">Dimethyl +0,+6 (Peptide Labeled)</option>
      <option value="Dimethyl +0,+8 (Peptide Labeled)">Dimethyl +0,+8 (Peptide Labeled)</option>
      <option value="Dimethyl +0,+4,+8 (Peptide Labeled)">Dimethyl +0,+4,+8 (Peptide Labeled)</option>
      <option value="Proteolytic O-18 labeling">Proteolytic O-18 labeling</option>
      <option value="Cleavable ICAT">Cleavable ICAT</option>
      <option value="ICPL Light, Heavy (Peptide Labeled)">ICPL Light, Heavy (Peptide Labeled)</option>
      <option value="ICPL Light, Heavy (Protein Labeled)">ICPL Light, Heavy (Protein Labeled)</option>
      <!-- TODO: Handle additional mTRAQ and iTRAQ options. 
      handle TMT (doesn't seem like UI lets quantatate these)
      <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
      <UI_QUANT_TYPE></UI_QUANT_TYPE>
      
      <UI_SAMPLE_TYPE></UI_SAMPLE_TYPE>
      <UI_QUANT_TYPE></UI_QUANT_TYPE>

      <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
      <UI_QUANT_TYPE></UI_QUANT_TYPE>

      <UI_SAMPLE_TYPE>TMT ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
      <UI_QUANT_TYPE></UI_QUANT_TYPE>
    -->
      <option value="SILAC unlabeled, N-15 labeled">SILAC unlabeled, N-15 labeled</option>
    </param>
    <param type="select" name="cys_alkylation" label="Cys Alkylation">
      <option value="None">None</option>
      <option value="Iodoacetamide">Iodoacetamide</option>      
      <option value="MMTS">MMTS</option>
      <option value="Acrylamide">Acrylamide</option>
      <option value="Iodoacetic acid">Iodoacetic acid</option>
      <option value="Iodoethanol">Iodoethanol</option>
      <option value="Vinylpyridine">Vinylpyridine</option>
      <option value="N-Ethylmaleimide">N-Ethylmaleimide</option>
      <option value="N-Methylmaleimide">N-Methylmaleimide</option>
      <option value="Iodoacetyl-PEO-Biotin">Iodoacetyl-PEO-Biotin</option>
      <option value="Iodoacetamide with Iodoacetyl-PEO-Biotin chase">Iodoacetamide with Iodoacetyl-PEO-Biotin chase</option>
      <option value="Iodoacetamide w other Cys mods possible">Iodoacetamide w other Cys mods possible</option>
      <option value="MMTS w other Cys mods possible">MMTS w other Cys mods possible</option>
      <option value="Unknown">Unknown</option>
    </param>
    <param type="select" name="digestion" label="Digestion">
      <option value="Trypsin">Trypsin</option>
      <option value="Glu C">Glu C</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="CNBr">CNBr</option>
      <option value="Lys C">Lys C</option>
      <option value="Acid Cleavage">Acid Cleavage</option>
      <option value="Arg C">Arg C</option>
      <option value="Asp N">Asp N</option>
      <option value="Lys N">Lys N</option>
      <option value="Thermolysin">Thermolysin</option>
      <option value="Trypsin + Chymotrypsin">Trypsin + Chymotrypsin</option>
      <option value="Trypsin + Glu C">Trypsin + Glu C</option>
      <option value="Trypsin + Asp N">Trypsin + Asp N</option>
      <option value="Lys C + Chymotrypsin">Lys C + Chymotrypsin</option>
      <option value="Lys C + Glu C">Lys C + Glu C</option>
      <option value="Glu C + Asp N">Glu C + Asp N</option>
      <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option>
      <option value="None">None</option>
    </param>
    <param type="select" name="instrument" label="Instrument">
      <option value="TripleTOF 5600">TripleTOF 5600</option>
      <option value="TripleTOF 4600">TripleTOF 4600</option>
      <option value="5800">5800</option>
      <option value="4800">4800</option>
      <option value="4700">4700</option>
      <option value="QSTAR Elite ESI">QSTAR Elite ESI</option>
      <option value="QSTAR Elite">QSTAR Elite</option>
      <option value="QSTAR oMALDI">QSTAR oMALDI</option>
      <option value="6500 QTRAP ESI">6500 QTRAP ESI</option>
      <option value="4500 QTRAP ESI">4500 QTRAP ESI</option>
      <option value="5500 QTRAP ESI">5500 QTRAP ESI</option>
      <option value="4000 QTRAP ESI">4000 QTRAP ESI</option>
      <option value="QTRAP ESI">QTRAP ESI</option>
      <option value="4000 QTRAP AP-MALDI">4000 QTRAP AP-MALDI</option>
      <option value="3200 QTRAP AP-MALDI">3200 QTRAP AP-MALDI</option>
      <option value="LTQ">LTQ</option>
      <option value="Orbi/FT MS (1-3ppm), LTQ MS/MS">Orbi/FT MS (1-3ppm), LTQ MS/MS</option>      
      <option value="Orbi/FT MS (sub-ppm), LTQ MS/MS">Orbi/FT MS (sub-ppm), LTQ MS/MS</option>
      <option value="Orbi MS, Orbi MS/MS">Orbi MS, Orbi MS/MS</option>
      <option value="Orbi MS (sub-ppm), Orbi MS/MS">Orbi MS (sub-ppm), Orbi MS/MS</option>
    </param>
    <conditional name="factors">
      <param name="factors_use" type="boolean" label="Specify Special Factors?" help="" truevalue="true" falsevalue="false" />
      <when value="false" />
      <when value="true">
        <param type="select" name="special_factors" label="Special Factors" display="checkboxes" multiple="true" help="">
          <option value="Phosphorylation emphasis">Phosphorylation emphasis</option>
          <option value="Methyl esterification">Methyl esterification</option>
          <option value="Phos-Tyr affinity column">Phos-Tyr affinity column</option>
          <option value="Gel-based ID">Gel-based ID</option>
          <option value="Urea denaturation">Urea denaturation</option>
          <option value="Acetylation emphasis">Acetylation emphasis</option>
          <option value="Ubiquitin/SUMO enrichment">Ubiquitin/SUMO enrichment</option>
          <option value="BONCAT workflow">BONCAT workflow</option>
          <option value="PNGase F in O-18 water">PNGase F in O-18 water</option>
          <option value="Pronota">Pronota</option>
          <option value="O-methylisourea treatment">O-methylisourea treatment</option>
          <option value="Purified Histones">Purified Histones</option>
          <option value="Propionylation pre-digestion">Propionylation pre-digestion</option>
          <option value="Propionylation post-digestion">Propionylation post-digestion</option>
          <option value="Deuteroacetylation pre-digestion">Deuteroacetylation pre-digestion</option>
          <option value="Deuteroacetylation post-digestion">Deuteroacetylation post-digestion</option>
          <option value="Iodo and Thyroxine mods enrichment">Iodo and Thyroxine mods enrichment</option>
        </param>
      </when>
    </conditional>
    <param format="fasta" name="database" type="data" label="Database" />
    <param name="quantitative" type="boolean" truevalue="True" falsevalue="False" label="Run Quantitation (if applicable)" checked="False" help="" />    
    <param name="background_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Background Correction (if applicable)" checked="False" help="" />
    <param name="bias_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Bias Correction (if applicable)" checked="False" help="" />
    <param type="select" name="search_foci" label="Search Focus" display="checkboxes" multiple="true" help="">
      <option value="Biological modifications">Biological modifications</option>
      <option value="Amino acid substitutions">Amino acid substitutions</option>
    </param>
    <param name="search_effort" type="boolean" truevalue="Thorough" falsevalue="Rapid" label="Thorough Search" checked="True" help="" />
    <param name="pspep" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use PSPEP" checked="True" help="" />
    <param type="select" name="min_unused_protscore" label="Detected Protein Threshold [Unused ProtScore (Conf)]">
      <option value="3.0">3.0 (99.9)</option>
      <option value="2.0">2.0 (99.0%)</option>
      <option value="1.3">1.3 (95.0%)</option>
      <option value="1.0">1.0 (90.0%)</option>
      <option value="0.70">0.70 (80.0%)</option>
      <option value="0.47">0.47 (66.0%)</option>
      <option value="0.10">0.10 (20.0%)</option>
      <option value="0.05" selected="true">0.05 (10.0%)</option>
    </param>
  </inputs>
  <outputs>
    <data format="group" name="output" label="ProteinPilot results for ${on_string}"/>
    <data format="xml" name="output_methods" label="ProteinPilot methods xml for ${on_string}" />
    <data format="xlsx" name="output_pspep_report" label="ProteinPilot PSPEP Report for ${on_string}">
      <filter>pspep</filter>
    </data>
  </outputs>
  <help>
  </help>
</tool>