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diff proteinpilot.xml @ 8:0aa9d080713e

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Update for ProteinPilot version 5.0
author Jim Johnson <jj@umn.edu>
date Thu, 05 Nov 2015 13:15:48 -0600
parents 790d80981060
children
line wrap: on
line diff
--- a/proteinpilot.xml	Mon Oct 20 15:54:33 2014 -0500
+++ b/proteinpilot.xml	Thu Nov 05 13:15:48 2015 -0600
@@ -1,199 +1,205 @@
-<tool id="proteinpilot" version="0.2.1" name="ProteinPilot">
-  <description></description>
-  <!-- ESCAPE input and database name -->
-  <configfiles>
-    <configfile name="input_config">## Describe input groups
+<tool id="proteinpilot" name="ProteinPilot" version="5.0.0">
+    <description></description>
+    <!-- ESCAPE input and database name -->
+    <command interpreter="python">
+<![CDATA[
+        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>
+    <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>
+        </configfile>
+    </configfiles>
+    <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>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>
+            <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>
-      </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>
+        <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>
+<![CDATA[
+
+]]>
+    </help>
 </tool>