# HG changeset patch
# User iracooke
# Date 1445388324 14400
# Node ID 0746a2ae9e04cdd18627e56dc1bca708602ece01
# Parent  d90c8bc10a9cc73ec6b6c0e2e454a153fe981391
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

diff -r d90c8bc10a9c -r 0746a2ae9e04 interprophet.xml
--- a/interprophet.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/interprophet.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,59 +1,71 @@
-<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
-	
-	<requirements>
-         <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-	    <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
-   </requirements>
-
-
-  <description>Combine Peptide Prophet results from multiple search engines</description>
-
-  <command>interprophet.rb --galaxy
+<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1">
+    <description>Combine Peptide Prophet results from multiple search engines</description>
+    <requirements>
+         <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        interprophet.rb --galaxy
+        #if str( $input_type.type ) == "files":
+            #for $pepxml_file in $input_type.pepxml_files:
+                ${pepxml_file}
+            #end for
+        #else
+            #for $list_item in $input_type.pepxml_list:
+                ${list_item}
+            #end for
+            #for $extra_list_holder in $input_type.extra_pepxml_lists:
+                #for $list_item in $extra_list_holder.extra_list:
+                    ${list_item}
+                #end for
+            #end for
+        #end if
 
-	-o interprophet_output.pep.xml
-
-	$use_nss 
-
-	$use_nrs 
-
-	$use_nse 
-
-	$use_nsi 
-
-	$use_nsm 
-
-	--p-thresh $p_thresh
+            -o interprophet_output.pep.xml
+            $use_nss
+            $use_nrs
+            $use_nse
+            $use_nsi
+            $use_nsm
+            --p-thresh $p_thresh
+            --threads "\${GALAXY_SLOTS:-12}"
 
-	--threads $threads
-
-#for $pepxml_file in $pepxml_files:
-	${pepxml_file}
-#end for	
-
-  </command>
-
-
-  <inputs>
-
-	<param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+]]>
+    </command>
+    <inputs>
 
-	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/>
-	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/>
-	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/>
-	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/>
-	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/>
-	
-    <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+        <conditional name="input_type">
+            <param name="type" type="select" label="Input Type">
+                <option value="files" selected="true">Datasets</option>
+                <option value="collections">Collections</option>
+            </param>
+            <when value="files">
+                <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+            </when>
+            <when value="collections">
+                <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+                <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" >
+                    <param name="extra_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+                </repeat>
+            </when>
+        </conditional>
 
-	<param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
-		
-  </inputs>
-  <outputs>
-    <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
-  </outputs>
+        <!-- <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> -->
 
- <help>
+        <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/>
+        <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/>
+        <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/>
+        <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/>
+        <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/>
+        <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+
+    </inputs>
+    <outputs>
+        <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/>
+    </outputs>
+    <help>
 
 **What it does**
 
@@ -67,6 +79,5 @@
 
 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
 
-  </help>
-
+    </help>
 </tool>
diff -r d90c8bc10a9c -r 0746a2ae9e04 peptide_prophet.xml
--- a/peptide_prophet.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/peptide_prophet.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,73 +1,66 @@
-<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0">
+<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.1">
+    <description>Calculate Peptide Prophet statistics on search results</description>
     <requirements>
-        <container type="docker">iracooke/protk-1.4.1</container>
-        <requirement type="package" version="1.4">protk</requirement>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
         <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
-   </requirements>
-   
-	<description>Calculate Peptide Prophet statistics on search results</description>
-
-	<command>
-        peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml
-
-        -r 
-        $glyco 
-        $useicat 
-        $phospho 
-        $usepi 
-        $usert 
-        $accurate_mass 
-        $no_ntt 
-        $no_nmc 
-        $use_gamma 
-        $use_only_expect 
-        $force_fit 
-        $allow_alt_instruments 
-        $maldi
-        $usedecoys
-        --decoy-prefix $decoy_prefix_string
-
-#if $experiment_label
-        --experiment-label $experiment_label
-#end if
+    </requirements>
+    <command>
+        peptide_prophet.rb
+            --galaxy $input_file
+            -o peptide_prophet_output.pep.xml
+            -r 
+            $glyco 
+            $useicat 
+            $phospho 
+            $usepi
+            $usert
+            $accurate_mass
+            $no_ntt
+            $no_nmc
+            $use_gamma
+            $use_only_expect
+            $force_fit
+            $allow_alt_instruments
+            $maldi
+            $usedecoys
+            --decoy-prefix $decoy_prefix_string
 
-        --p-thresh $p_thresh
-
-        --threads $threads
-
-	</command>
-
-	<inputs>
-	
-    <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/>
+            #if $experiment_label
+                --experiment-label $experiment_label
+            #end if
 
-	<param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>
-	<param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/>
-	<param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>
-	<param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>
-	<param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>
-	<param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>
-	<param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/>
-	<param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/>
-	<param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/>
-	<param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. 
-        Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
-	<param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/>
-	<param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/>
-	<param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
-    <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>
-    <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/>	
-    <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>
-    <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
-    <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
-	
-  </inputs>
-  <outputs>
-    <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/>
-  </outputs>
+            --p-thresh $p_thresh
+            --threads "\${GALAXY_SLOTS:-12}"
 
 
-<help>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/>
+
+        <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>
+        <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/>
+        <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>
+        <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>
+        <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>
+        <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>
+        <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/>
+        <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/>
+        <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/>
+        <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. 
+            Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>
+        <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/>
+        <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/>
+        <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>
+        <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>
+        <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/>    
+        <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>
+        <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+    </inputs>
+    <outputs>
+        <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/>
+    </outputs>
+    <help>
 
 **What it does**
 
@@ -82,7 +75,7 @@
 Keller A., et al. “Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search” *Anal. Chem.* 74, 5383-5392 (2002).
 
 
-</help>
+    </help>
 
 
 <!--PeptideProphet options [following the 'O']:
diff -r d90c8bc10a9c -r 0746a2ae9e04 pepxml_to_table.xml
--- a/pepxml_to_table.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/pepxml_to_table.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,45 +1,30 @@
-<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0">
-
-	<requirements>
-            <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-   </requirements>
-
-
-
-  <description>Converts a pepXML file to a tab delimited text file</description>
-
-
-<!-- Note .. the input file is assumed to be the first argument -->
-<command>pepxml_to_table.rb $input_file -o $output $invert_probs</command>
-
-
-<inputs>
-
-	<param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
-    <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
-
-</inputs>
-<outputs>
-	<data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
-</outputs>
-
-	
-	<tests>
-	  <!-- Just test that the tool runs and produces vaguely correct output -->
-	  <test>
-	      <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/>
-	      <output name="output" format="csv">
-	          <assert_contents>
-	              <has_text text="ANTNNYAPKSSR" />
-	          </assert_contents>
-	      </output>
-	  </test>
-	</tests>
-
-
+<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1">
+    <description>Converts a pepXML file to a tab delimited text file</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <!-- Note .. the input file is assumed to be the first argument -->
+    <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command>
+    <inputs>
+        <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
+        <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
+    </outputs>
+    <tests>
+        <!-- Just test that the tool runs and produces vaguely correct output -->
+        <test>
+            <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/>
+            <output name="output" format="csv">
+                <assert_contents>
+                    <has_text text="ANTNNYAPKSSR" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
 <help>
-	Convert a pepXML file to Tab delimited text
+    Convert a pepXML file to Tab delimited text
 </help>
-
 </tool>
diff -r d90c8bc10a9c -r 0746a2ae9e04 protein_prophet.xml
--- a/protein_prophet.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/protein_prophet.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,79 +1,73 @@
-<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.0">
-	<requirements>
-            <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-	    <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
-   </requirements>
-
-  <description>Calculate Protein Prophet statistics on search results</description>
-
+<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.1">
+    <description>Calculate Protein Prophet statistics on search results</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+    </requirements>
 
-<!-- Note .. the input file is assumed to be the first argument -->
-  <command>
-  	protein_prophet.rb
-
-  	--galaxy $input_file 
-
-  	-o protein_prophet_results.prot.xml
-
-  	-r
+    <command>
+        protein_prophet.rb
+            --galaxy 
+            
+            #for $input_file in $input_files:
+                ${input_file}
+            #end for
+            
+            -o protein_prophet_results.prot.xml
+            -r
 
-  	$iproph 
-  	$nooccam 
-  	$groupwts 
-  	$normprotlen 
-  	$logprobs 
-  	$confem 
-  	$allpeps 
-  	$unmapped 
-  	$instances 
-  	$delude
-  	
-  	--minprob=$minprob 
-  	--minindep=$minindep 
-  </command>
-  <inputs>
-	
-    <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>
+            $iproph
+            $nooccam
+            $groupwts
+            $normprotlen
+            $logprobs
+            $confem
+            $allpeps
+            $unmapped
+            $instances
+            $delude
+          --minprob=$minprob
+          --minindep=$minindep
+    </command>
+    <inputs>
+        <param name="input_files" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="true" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>
 
-	<param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>
-	<param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/>
-	<param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/>
-	<param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>
-	<param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>
-	<param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>
-	<param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>
-	<param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>
-	<param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>
-	<param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>
+        <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>
+        <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/>
+        <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/>
+        <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>
+        <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>
+        <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>
+        <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>
+        <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>
+        <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>
+        <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>
 
-	<param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>
-	<param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>
-	
-  </inputs>
-  <outputs>
-    <data format="protxml" name="output" metadata_source="input_file" label="protein_prophet.${input_file.display_name}.protXML" from_work_dir="protein_prophet_results.prot.xml"/>
-  </outputs>
+        <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>
+        <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>
+    </inputs>
+    <outputs>
+        <data format="protxml" name="output" from_work_dir="protein_prophet_results.prot.xml"/>
+    </outputs>
 
 
 <!--NOPLOT: do not generate plot png file
-		NOOCCAM: non-conservative maximum protein list
-		GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold)   
-		NORMPROTLEN: Normalize NSP using Protein Length
-		LOGPROBS: Use the log of the probabilities in the Confidence calculations
-		CONFEM: Use the EM to compute probability given the confidence 
-		ALLPEPS: Consider all possible peptides in the database in the confidence model
-		UNMAPPED: Report results for UNMAPPED proteins
-		INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
-		DELUDE: do NOT use peptide degeneracy information when assessing proteins
-		
-		MINPROB: peptideProphet probabilty threshold (default=0.05) 
-		MININDEP: minimum percentage of independent peptides required for a protein (default=0) 
-		
-		
+        NOOCCAM: non-conservative maximum protein list
+        GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold)   
+        NORMPROTLEN: Normalize NSP using Protein Length
+        LOGPROBS: Use the log of the probabilities in the Confidence calculations
+        CONFEM: Use the EM to compute probability given the confidence 
+        ALLPEPS: Consider all possible peptides in the database in the confidence model
+        UNMAPPED: Report results for UNMAPPED proteins
+        INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
+        DELUDE: do NOT use peptide degeneracy information when assessing proteins
+        
+        MINPROB: peptideProphet probabilty threshold (default=0.05) 
+        MININDEP: minimum percentage of independent peptides required for a protein (default=0) 
 -->
 
-  <help>
+    <help>
 
 **What it does**
 
@@ -88,6 +82,5 @@
 Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003).
 
 
-  </help>
-
+    </help>
 </tool>
diff -r d90c8bc10a9c -r 0746a2ae9e04 protxml_to_table.xml
--- a/protxml_to_table.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/protxml_to_table.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,49 +1,37 @@
-<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.0">
-	<requirements>
-            <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-   </requirements>
-
-	<description>Converts a ProtXML file to a table</description>
-
-	<command>
-		protxml_to_table.rb 
-	  	$invert_probs
-
-		$input_file 
-		-o $output 
-	</command>
-
-	<inputs>	
-		
-		<param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
-	    <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
-	</inputs>
-
-
-	<outputs>
-		<data format="tabular" name="output" />
-	</outputs>
-
-	<tests>
-	  <!-- Just test that the tool runs and produces vaguely correct output -->
-	  <test>
-	      <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/>
-	      <output name="output" format="tabular">
-	          <assert_contents>
-	              <has_text text="AVQKYLTAHEQSK" />
-	          </assert_contents>
-	      </output>
-	  </test>
-	</tests>
-
-
-  <help>
-
+<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1">
+    <description>Converts a ProtXML file to a table</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <command>
+        protxml_to_table.rb
+          $invert_probs
+        $input_file
+        -o $output
+    </command>
+    <inputs>
+        <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
+        <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+      <!-- Just test that the tool runs and produces vaguely correct output -->
+      <test>
+          <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/>
+          <output name="output" format="tabular">
+              <assert_contents>
+                  <has_text text="AVQKYLTAHEQSK" />
+              </assert_contents>
+          </output>
+      </test>
+    </tests>
+    <help>
 **What it does**
 
 Converts a ProtXML file to a tab separated table 
 
-  </help>
-
+    </help>
 </tool>
diff -r d90c8bc10a9c -r 0746a2ae9e04 repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Mar 26 19:55:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Proteomics datatypes">
-    <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
- </repositories>
diff -r d90c8bc10a9c -r 0746a2ae9e04 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="protk" version="1.4.3">
+        <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.8.0">
+        <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>