--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpqonvert.xml	Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,217 @@
+<tool id="idpQonvert" name="idpQonvert" version="0.1.0">
+  <!-- TODO: Set defaults for weights correctly -->
+  <description>
+    Prepare identification results for IDPicker.
+  </description>
+  <command>
+  #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+  #set $input_name = $input.display_name
+  #set $output_name = $input_name.split(".")[0] + ".idpDB"
+  ln -s '$input' '${input_name}';
+  ln -s '$input_database' '${db_name}';
+  idpQonvert -DecoyPrefix '${decoy_prefix}' \
+  -WriteQonversionDetails true \
+  -ProteinDatabase '${db_name}' \
+  -MaxFDR $max_fdr \
+  -EmbedSpectrumScanTimes false \
+  -EmbedSpectrumSources false \
+  #if $scoring.override_scoring
+  #set $score_info = []
+  #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
+  #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
+  #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
+  #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
+  #continue
+  #end for
+  #set $score_str = "; ".join($score_info)
+  -ScoreInfo '$score_str' \
+  #end if  
+  #if $advanced_options.use_advanced_options
+  -MaxImportFDR $advanced_options.max_import_fdr \
+  -MaxResultRank $advanced_options.max_result_rank \ 
+  -RerankMatches $advanced_options.rerank_matches \
+  -Gamma $advanced_options.gamma \
+  -Nu $advanced_options.nu \
+  -PolynomialDegree $advanced_options.polynomial_degree \
+  -TruePositiveThreshold $advanced_options.true_positive_threshold \
+  -MaxTrainingRank $advanced_options.max_training_rank \
+  -SVMType $advanced_options.svm_type \ 
+  -Kernel $advanced_options.kernel \ 
+  -ChargeStateHandling $advanced_options.charge_state_handling \ 
+  -QonverterMethod $advanced_options.qonverter_method \
+  -MinPartitionSize $advanced_options.min_partition_size \
+  #end if
+  '${input_name}';
+  mv '$output_name' output
+  </command>
+<!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
+-->
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+    <regex match="^Could not find the default configuration file.*$"
+      source="both"
+      level="warning" />
+  </stdio>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzid">mzIdentML</option>
+        <option value="pepXML">pepXML</option>
+      </param>
+      <when value="mzid">
+        <param format="mzid" name="input" type="data" label="Input mzIdentML"/>
+      </when>
+      <when value="pepXML">
+        <param format="pepXML" name="input" type="data" label="Input pepXML"/>
+      </when>
+    </conditional>
+    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
+    <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
+    <param name="max_fdr" type="float" label="Max FDR" value="0.05" />
+	<conditional name="advanced_options">
+      <param name="use_advanced_options" type="boolean" truevalue="true" falsevalue="false" label="Set Advanced Options" help="" />
+      <when value="false" />          
+      <when value="true">
+        <param name="max_import_fdr" type="float" label="Max Import FDR" value="0.25" />
+        <param name="max_result_rank" type="integer" label="Max Result Rank" value="3" />
+        <param name="max_training_rank" type="integer" label="Max Training Rank" value="1" />
+        <param name="rerank_matches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
+	    <param name="gamma" type="float" label="Gamma" value="5" />
+        <param name="nu" type="float" label="Nu" value="-0.5" />
+		<param name="true_positive_threshold" type="float" label="True Positive Threshold" value="0.01" />
+        <param name="polynomial_degree" type="integer" label="Polynomial Degree" value="3" />
+        <param name="min_partition_size" type="integer" label="Minimum Partition Size" value="10" />
+		<param name="svm_type" label="SVM Type" type="select">
+		  <option value="CSVC" selected="true">CSVC</option>
+		  <option value="NuSVC">Nu SCV</option>
+		  <option value="OneClass">One Class</option>
+		  <option value="NuSVR">Nu SVR</option>
+		  <option value="EpsilonSVR">Epsilon SVR</option>
+	    </param>	    
+		<param name="kernel" label="Kernel" type="select">
+		  <option value="Linear" selected="true">Linear</option>
+		  <option value="Polynomial">Polynomial</option>
+		  <option value="RBR">Radial Basis Function</option>
+		  <option value="Sigmoid">Sigmoid</option>
+	    </param>
+	    <param name="charge_state_handling" label="Charge State Handling" type="select">
+		  <option value="Partition" selected="true">Partition</option>
+		  <option value="Ignore">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="terminal_specificity_handling" label="Terminal Specificity Handling" type="select">
+		  <option value="Partition" selected="true">Partition</option>
+		  <option value="Ignore">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
+		  <option value="Ignore" selected="true">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
+		  <option value="Ignore" selected="true">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="mass_error_handling" label="Mass Error Handling" type="select">
+		  <option value="Ignore" selected="true">Ignore</option>
+		  <option value="Feature">Feature</option>
+	    </param>
+	    <param name="qonverter_method" label="Qonverter Method" type="select">
+		  <option value="MonteCarlo" selected="true">Monte Carlo</option>
+		  <option value="SingleSVM">SVM (single)</option>
+		  <option value="PartitionSVM">SVM (parition)</option>
+		  <option value="StaticWeighted">Static Weighted</option>
+	    </param>
+      </when>
+    </conditional>
+    <conditional name="scoring">
+      <param name="override_scoring" type="boolean" truevalue="true" falsevalue="false" label="Modify Search Application Weights" />
+      <when value="false" />
+      <when value="true">
+      	<param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" value="1" />
+		<param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>
+	    <param name="xcorr_weight" label="XCorr Weight" type="float" value="1" />
+		<param name="xcorr_type" label="XCorr Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>
+      	<param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" value="1" />
+		<param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+	    <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" value="1" />
+		<param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>
+        <param name="mascot_score_weight" label="Mascot Score Weight" type="float" value="1" />
+		<param name="mascot_score_type" label="Mascot Score Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+        <param name="xtandem_expect_weight" label="X! Tandem (Expectation) Weight" type="float" value="-1" />
+		<param name="xtandem_expect_type" label="X! Tandem (Expectation) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+        <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" value="1" />
+		<param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+        <param name="ms-gf_spacevalue_weight" label="MS-GF (spacevalue) Weight" type="float" value="-1" />
+		<param name="ms-gf_spacevalue_type" label="MS-GF (spacevalue) Normalization" type="select">
+		  <option value="off" selected="true">None</option>
+		  <option value="quantile">Quantile</option>
+		  <option value="linear">Linear</option>
+	    </param>	    
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="idpdb" name="output" from_work_dir="output" />
+  </outputs>
+  <requirements>
+    <requirement type="package" version="3.0.475">idpQonvert</requirement>
+  </requirements>
+  <help>
+**What it does**
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+  </help>
+</tool>
+<!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
+
+idpQonvert -OverwriteExistingFiles true -MaxFDR 0.05 -MaxImportFDR 0.25  -MaxResultRank 3 -RerankMatches false -TruePositiveThreshold 0.01 -MaxTrainingRank 1 -Gamma 5 -Nu -0.5 -PolynomialDegree 3 -ScoreInfo "1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off xexpect; 1 off x\!tandem:hyperscore; -1 off ms-gf:specevalue" -SVMType CSVC -Kernel Linear -ChargeStateHandling Partition -QonverterMethod MonteCarlo -MinPartitionSize 10 -DecoyPrefix RRRRRR -ProteinDatabase test2.fasta input.pepXML
+
+
+ScoreInfo: 1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off x!tandem:expect; 1 off x!tandem:hyperscore; -1 off ms-gf:specevalue
+
+off is normalization: quantile, linear, or off
+
+SVMType: CSVC, NuSVC, OneClass, EpsilonSVR, NuSVR
+Kernel: Linear, Polynomial, RBF (radial basis function), Sigmoid
+ChargeStateHandling: Parition, Ignore, Feature
+TerminalSpecificityHandling: Partition, Ignore, Feature
+MissedCleavagesHandling: Ignore, Feature
+MassErrorHandling: Ignore, Feature
+QonverterMethod: MonteCarlo, SingleSVM, PartitionedSVM, StaticWeighted
+
+-->