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Initial commit.
author galaxyp
date Fri, 10 May 2013 17:06:14 -0400
parents
children b9a850d6cc47
files LICENSE README.md README_GALAXYP.md README_REPO.md idpicker.xml idpicker_wrapper.py idpqonvert.xml myrimatch.xml tagrecon.xml update.sh
diffstat 10 files changed, 989 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,202 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,25 @@
+This repository contains tool wrappers for the Tabb lab tools
+idqonvert, myrimatch, and tagrecon. There is also an IDPicker3 tool
+wrapper, but it does not work due to bugs in IDPicker3's file merging
+functionality.# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,22 @@
+# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,4 @@
+This repository contains tool wrappers for the Tabb lab tools
+idqonvert, myrimatch, and tagrecon. There is also an IDPicker3 tool
+wrapper, but it does not work due to bugs in IDPicker3's file merging
+functionality.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,56 @@
+<tool id="idpicker" name="IDPicker 3" version="0.1.0">
+  <description>
+    Assemble parsimonious protien identifications.
+  </description>
+  <configfiles>
+    <configfile name="group_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
+#for $group in $groups:
+group:$group.group_name
+#for $idpdb_input in $group.idpdb_inputs:
+name:${idpdb_input.display_name}
+path:${idpdb_input}
+#end for
+#end for
+    </configfile>
+  </configfiles>
+  <command interpreter="python">
+    idpicker_wrapper.py --input $group_config --output $output
+  </command>
+  <inputs>
+    <param format="idpdb" name="outside_inputs" type="data" multiple="true" label="idpDB Inputs" help="Run results through idpQonvert tool to produce idpDB files for IDPicker." />
+    <repeat name="groups" title="Experimental Group">
+      <param name="group_name" type="text" label="Group Name" help="Name for the group (use only letters and numbers)." />
+      <param format="idpdb" name="idpdb_inputs" type="data" multiple="true" label="idpDB Inputs" help="Run results through idpQonvert tool to produce idpDB files for IDPicker." />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="idpdb" name="output" />
+  </outputs>
+  <requirements>
+    <requirement type="package">idpicker</requirement>
+  </requirements>
+  <help>
+**WARNING**
+
+This tool does not current work.
+
+**What it does**
+
+
+
+** Building Groups **
+
+Build arbitrary hierarchy by nesting groups with colon (e.g. control:666Gx6).
+
+http://fenchurch.mc.vanderbilt.edu/bumbershoot/idpicker/index_files/image003.gif
+
+------
+
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+  </help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker_wrapper.py	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+import optparse
+import sys
+import os
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(-1)
+
+
+def build_groups(input):
+    os.makedir("input_directory")
+
+
+def main():
+    parser = optparse.OptionParser()
+    parser.add_option('--input')
+    parser.add_option('--output')
+    (options, args) = parser.parse_args()
+    if not len(options.input):
+        stop_err("No input file found")
+    build_groups(options.input)
+
+if __name__ == '__main__':
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpqonvert.xml	Fri May 10 17:06:14 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">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
+
+-->
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/myrimatch.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,192 @@
+<tool id="myrimatch" name="myrimatch" version="0.1.0">
+  <description></description>
+  <command>
+  #set $mod_rep_chars = "*$^@.%!"
+  #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+  #if $output_type.value == "mzid"
+  #set $output_ext="mzid"
+  #set $output_format="mzIdentML"
+  #else 
+  #set $output_ext="pepXML"
+  #set $output_format="pepXML"
+  #end if
+  #set $input_name = $input.display_name
+  #set $output_name = $input_name.split(".")[0] + "." + $output_ext
+  #set $static_mods_str = ""
+  #for $static_mod in $static_mods
+  #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass)
+  #end for
+  #set $dynamic_mods_str = ""
+  #set $dynamic_mod_index = 0
+  #for $dynamic_mod in $dynamic_mods
+  #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass)
+  #set $dynamic_mod_index = $dynamic_mod_index + 1
+  #end for
+  ln -s '$input' '${input_name}';
+  ln -s '$input_database' '${db_name}';
+  myrimatch -DecoyPrefix '${decoy_prefix}' \
+  -ProteinDatabase '${db_name}' \
+  -OutputFormat '${$output_format}' \
+  '${input_name}' \
+  -StaticMods '${static_mods_str}' \
+  -DynamicMods '${dynamic_mods_str}' \
+  -CleavageRules '${protease}' \
+  #set $percursor_type = $percursor_tolerance.percursor_type
+  -PrecursorMzToleranceRule '${percursor_type}' \
+  #if $percursor_type == "auto" or $percursor_type == "mono"
+  -MonoPrecursorMzTolerance '${percursor_tolerance.mono_precursor_mz_tolerance}${percursor_tolerance.mono_precursor_mz_tolerance_units}' \
+  #end if
+  #if $percursor_type == "auto" or $percursor_type == "avg"
+  -AvgPrecursorMzTolerance '${percursor_tolerance.avg_precursor_mz_tolerance}${percursor_tolerance.avg_precursor_mz_tolerance_units}' \
+  #end if
+  -FragmentMzTolerance '${fragment_mz_tolerance}${fragment_mz_tolerance_units}' \
+  #if $advanced.use_advanced
+  -UseSmartPlusThreeModel $advanced.use_smart_plus_three_model \
+  -MinPeptideLength $advanced.min_peptide_length \
+  -MaxPeptideLength $advanced.max_peptide_length \
+  #if $advanced.max_peak_count
+  -MaxPeakCount $advanced.max_peak_count \
+  #end if
+  #if $advanced.fragmentation_rule.override
+  -FragmentationAutoRule false -FragmentationRule 'manual:${advanced.fragmentation_rule.fragmentation_rule}' \
+  #end if
+  #end if
+  ;
+  mv '$output_name' output
+  </command>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+    <regex match="^Could not find the default configuration file.*$"
+      source="both"
+      level="warning" />
+  </stdio>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="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">
+        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+      </when>
+      <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>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="raw_pepxml">pepXML</option>
+      <option value="mzid">mzIdentML</option>
+    </param> 
+    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
+    <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
+    <param name="protease" type="select" label="Protease"> 
+      <options from_file="proteases.loc">
+        <column name="name" index="0" />
+        <column name="value" index="1" />
+      </options>
+    </param>    
+    <repeat name="static_mods" title="Static Modifications">
+      <param name="aa" type="text" label="Amino Acid" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <repeat name="dynamic_mods" title="Dynamic Modifications" max="7">
+      <param name="motif" type="text" label="Amino Acid Motif" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <conditional name="percursor_tolerance">
+      <param name="percursor_type" type="select" label="Percursor Mass Type" help="For data from Thermo instruments, using the 'auto' setting on a will automatically choose monoisotopic or average mass values, for other instruments monoisotopic or average should be chosen.">
+        <option value="auto">Auto</option>
+        <option value="avg">Average</option>
+        <option value="mono">Monoisotopic</option>
+      </param>
+      <when value="auto">
+        <param name="mono_precursor_mz_tolerance" type="float" value="10" label="Monoisotopic Percursor m/z Tolerance" />
+        <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons">Daltons</option>
+        </param>
+        <param name="avg_precursor_mz_tolerance" type="float" value="1.5" label="Average Percursor m/z Tolerance" />
+        <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons" selected="true">Daltons</option>          
+        </param>
+      </when>
+      <when value="avg">
+        <param name="avg_precursor_mz_tolerance" type="float" value="1.5" label="Average Percursor m/z Tolerance" />
+        <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons" selected="true">Daltons</option>          
+        </param>
+      </when>
+      <when value="mono">
+        <param name="mono_precursor_mz_tolerance" type="float" value="10" label="Monoisotopic Percursor m/z Tolerance" />
+        <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Percursor m/z Tolerance Units">
+          <option value="ppm">Parts per million</option>
+          <option value="daltons">Daltons</option>
+        </param>        
+      </when>
+    </conditional>
+    <param name="fragment_mz_tolerance" type="float" value="1.5" label="Fragement m/z Tolerance" />
+    <param name="fragment_mz_tolerance_units" type="select" label="Fragment m/z Tolerance Units">
+      <option value="ppm">Parts per million</option>
+      <option value="daltons" selected="true">Daltons</option>
+    </param>
+    <conditional name="advanced">
+      <param name="use_advanced" type="boolean" label="Set Advanced Options" />
+      <when value="false">
+      </when>
+      <when value="true">
+        <param name="max_peak_count" type="integer" value="" optional="true" label="Use Max Peaks" help="Filter out all but the specified number of peaks, keep empty to use all peaks." />
+        <conditional name="fragmentation_rule">
+          <param name="override" type="boolean" label="Override Fragmentation Rule (Ion Series)" />
+          <when value="false" />
+          <when value="true">
+            <param type="text" name="fragmentation_rule" label="Fragmentation Rule" help="specify as a comma-separated list of a, b, c, x, y, z, or z* (z+1), e.g. b,y,z" />
+          </when>
+        </conditional>
+        <param name="min_peptide_length" type="integer" value="5" label="Minimum Peptide Length" />
+        <param name="max_peptide_length" type="integer" value="75" label="Maximum Peptide Length" />
+        <param name="use_smart_plus_three_model" type="boolean" truevalue="true" falsevalue="false" label="Use Smart Plus 3 Model"  help="For +3 and higher precursors, the fragment ions predicted depend on the way this parameter is set. When this parameter is true, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. When this parameter is false, however, ALL possible charge distributions for the fragment ions are generated for every peptide bond." checked="true" />
+
+      </when>
+    </conditional>
+    <!--
+    <param name="max_peptide_length" value="75"
+
+    <param name="use_smart_plus_three_model" type="boolean" truevalue="true" falsevalue="false" label="Use Smart Plus 3 Model"  help="For +3 and higher precursors, the fragment ions predicted depend on the way this parameter is set. When this parameter is true, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. When this parameter is false, however, ALL possible charge distributions for the fragment ions are generated for every peptide bond." checked="true" />
+  -->
+  </inputs>
+  <outputs>
+    <data format="raw_pepxml" name="output" from_work_dir="output">
+      <change_format>
+        <when input="output_type" value="mzid" format="mzid" />
+      </change_format>
+    </data>
+  </outputs>
+
+  <requirements>
+    <requirement type="package">myrimatch</requirement>
+  </requirements>
+
+  <help>
+**What it does**
+
+Performs protein identification via database search using MyriMatch.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Tabb DL, Fernando CG, Chambers MC. J Proteome Res. 6(2) 654-61. 2007 Feb. PMCID PMC2525619`
+
+If you use this tool in Galaxy, please cite TODO
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tagrecon.xml	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,210 @@
+<tool id="tagrecon" name="TagRecon" version="0.1.0">
+  <description></description>
+  <command>    
+  #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+  #if $output_type.value == "mzid"
+  #set $output_ext="mzid"
+  #set $output_format="mzIdentML"
+  #else 
+  #set $output_ext="pepXML"
+  #set $output_format="pepXML"
+  #end if
+  #set $input_name = $input.display_name
+  #set $tags_name = $input_name.split(".")[0] + ".tags"
+  #set $output_name = $input_name.split(".")[0] + "." + $output_ext
+  #set $static_mods_str = ""
+  #for $static_mod in $static_mods
+  #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass)
+  #end for
+  #set $dynamic_mods_str = ""
+  #set $dynamic_mod_index = 0
+  #for $dynamic_mod in $dynamic_mods
+  #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass)
+  #set $dynamic_mod_index = $dynamic_mod_index + 1
+  #end for
+  ln -s '$input' '${input_name}';
+  ln -s '$input_database' '${db_name}';
+  cp \${TAGRECON_UNIMOD_PATH:-${GALAXY_DATA_INDEX_DIR}/unimod.xml} .;
+  cp \${TAGRECON_BLOSUM_PATH:-${GALAXY_DATA_INDEX_DIR}/blosum62.fas} .;
+  directag '${input_name}' \
+  -StaticMods '${static_mods_str}' \
+  -DynamicMods '${dynamic_mods_str}' \
+  -MaxDynamicMods '$max_dynamic_mods' \
+  -MaxResults ${max_tags} \
+  -FragmentMzTolerance ${tag_mz_tolerance} \
+  #if $advanced_charge_options.specify
+  -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \
+  #end if
+  #if $tag_weights.specify
+  -IntensityScoreWeight $tag_weights.intensity \
+  -MzFidelityScoreWeight $tag_weights.mz \
+  -ComplementScoreWeight $tag_weights.complement \
+  #end if
+  ;
+  tagrecon -DecoyPrefix '${decoy_prefix}' \
+  -ProteinDatabase '${db_name}' \
+  -OutputFormat '${$output_format}' \
+  -StaticMods '${static_mods_str}' \
+  -DynamicMods '${dynamic_mods_str}' \
+  -MaxDynamicMods '$max_dynamic_mods' \
+  -CleavageRules '${protease}' \
+  -MaxMissedCleavages ${max_missed_cleavages} \
+  #if $advanced_cleavage_options.specify
+  -MinTerminiCleavages $advanced_cleavage_options.min_termini_cleavages \
+  -UseNETAdjustment $advanced_cleavage_options.use_net_adjustment \
+  #end if
+  #if $advanced_charge_options.specify
+  -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \
+  #end if
+  #if $search_untagged.search
+  -SearchUntaggedSpectra true \
+  -UntaggedSpectraPrecMZTol $search_untagged.precursor_mz_tolerance
+  #end if
+  '${tags_name}';
+  mv '$output_name' output
+  </command>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+    <regex match="^Could not find the default configuration file.*$"
+      source="both"
+      level="warning" />
+  </stdio>
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="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">
+        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+      </when>
+      <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>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="raw_pepxml">pepXML</option>
+      <option value="mzid">mzIdentML</option>
+    </param> 
+    <param format="fasta" name="input_database" type="data" label="Protein Database"/>
+    <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
+    <repeat name="static_mods" title="Static Modifications (used by both directag and tagrecon) ">
+      <param name="aa" type="text" label="Amino Acid" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <repeat name="dynamic_mods" title="Dynamic Modifications  (used by both directag and tagrecon)" max="7">
+      <param name="motif" type="text" label="Amino Acid Motif" />
+      <param name="mass" type="float" label="Mass" value="0" />
+    </repeat>
+    <param name="max_dynamic_mods" type="integer" label="Maximum Dynamic Mods per Sequence" value="2" />
+    <param name="tag_length" type="integer" label="Tag Length" value="3" help="A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare." />
+    <param name="max_tags" type="integer" label="Maximum Number of Tags per Spectrum" value="20" />
+    <param name="tag_mz_tolerance" type="float" label="Fragment m/z Tolerance during Tag Generation (Da/z)" value=".5" />
+    <param name="protease" type="select" label="Protease"> 
+      <options from_file="proteases.loc">
+        <column name="name" index="0" />
+        <column name="value" index="1" />
+      </options>
+    </param>
+    <param name="max_missed_cleavages" label="Maximum Number of Missed Cleavages" type="integer" value="-1" />
+    <conditional name="advanced_cleavage_options">
+      <param name="specify" type="boolean" label="Specify advanced cleavage options" help="" truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="min_termini_cleavages" type="select" label="Minimum Termini Cleavages" value="2" help="A peptide must start after a cleavage and end before a cleavage. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified above.">
+          <option value="2">2</option>
+          <option value="1">1</option>
+          <option value="0">0</option>
+        </param>
+        <param name="use_net_adjustment" type="boolean" label="Use NET Adjustment" help="When enabled, TagRecon adds a probabilistic bonus to peptide scores depending on whether the peptides are fully-enzymatic, semi-enzymatic, or non-enzymatic." truevalue="true" falsevalue="false" />
+      </when>
+    </conditional>
+    <conditional name="advanced_charge_options">
+      <param name="specify" type="boolean" label="Specify Advanced Charge State Handling Options" help="" truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="use_ms_charge_state" type="boolean" label="Use Charge State from MS" truevalue="true" falsevalue="false" help="When enabled, DirecTag and TagRecon will not use their internal algorithm to determine charge state of a spectrum when it is available in the input file." />
+        <!-- TODO: Add DuplicateSpectra, NumChargeStates -->
+      </when>
+    </conditional>
+    <!-- TODO: Advanced Peptide Filtering: Min/Max Peptide Mass/Length -->
+    <conditional name="tag_weights">
+      <param name="specify" type="boolean" label="Override Default Tag Weighting" help="By default equal weights are assigned to intensity, m/z fidelity, and complement scores." truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="intensity" type="float" label="Intensity Score Weight" help="" value="1.0" />
+        <param name="mz" type="float" label="m/z Fidelity Score Weight" help="" value="1.0" />
+        <param name="complement" type="float" label="Complement Score Weight" help="" value="1.0" />
+      </when>
+    </conditional>
+    <conditional name="search_untagged">
+      <param name="search" type="boolean" label="Search Untagged Spectra" help="Search untagged spectra like a database search." truevalue="true" falsevalue="false" />
+      <when value="false" />
+      <when value="true">
+        <param name="precursor_mz_tolerance" type="float" label="Untagged Spectra Precursor m/z Tolerance" value="1.25" />
+      </when>
+    </conditional>
+    <conditional name="unknown_mass_shifts">
+      <param name="how" type="select" label="Explaination for Unknown Mass Shifts">
+        <option value="">None, disable delta mass interpretation by TagRecon</option>
+        <option value="blindptms">Blind PTMs</option>
+        <option value="mutations">Mutations</option>
+        <!-- TODO: Add preferredptms -->
+      </param>
+      <when value="blindptms">
+        <!-- BlindPTMResidues ??? -->
+      </when>
+      <when value="mutations">
+        <!-- BlosumScoreThreshold ??? BlosumThreshold ???-->
+      </when>
+      <when value="" />
+    </conditional>
+  </inputs>
+<!-- 
+  Both:
+  AdjustPrecursorMass (defaults to false)
+
+  TagRecon:
+  Skip for now: ComputeXCorr
+  Skip forever: ProteinSampleSize
+
+  TO ADD:
+
+  Both: Advanced, ClassSizeMultiplier, float 2.0.
+-->
+  <outputs>
+    <data format="raw_pepxml" name="output" from_work_dir="output">
+      <change_format>
+        <when input="output_type" value="mzid" format="mzid" />
+      </change_format>
+    </data>
+  </outputs>
+
+  <requirements>
+    <requirement type="package">directag</requirement>
+    <requirement type="package">tagrecon</requirement>
+  </requirements>
+
+  <help>
+**What it does**
+
+Performs protein identification via Directag and TagRecon.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`.
+
+If you use this tool in Galaxy, please cite TODO.
+  </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh	Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$LICENSE_FILE" ];
+then
+    wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE"
+fi
+
+# Run repository specific update actions.
+if [ -f update_repo.sh ];
+then
+    ./update_repo.sh
+fi
+
+wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md
+
+# Create repository README
+if [ ! -e README_REPO.md ];
+then
+    echo "TODO: Document this tool repository." > README_REPO.md
+fi
+cat README_REPO.md README_GALAXYP.md > README.md
+
+
+# If version file exists, update all tools to this version
+VERSION_FILE=version
+if [ -e "$VERSION_FILE" ];
+then
+    VERSION=`cat $VERSION_FILE`
+    
+    # Replace tool version in each tool XML file   `
+    find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \;
+
+fi