# HG changeset patch
# User galaxyp
# Date 1500072185 14400
# Node ID c221d1871982d228e4bd85001a6a718fe000d73b
# Parent  a6a6a9a850b5ccf2a9ff2e2b3d351fb1beb9420f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

diff -r a6a6a9a850b5 -r c221d1871982 FalseDiscoveryRate.xml
--- a/FalseDiscoveryRate.xml	Thu Apr 27 12:48:14 2017 -0400
+++ b/FalseDiscoveryRate.xml	Fri Jul 14 18:43:05 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.1.0">
+<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.2.0">
   <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
   <macros>
     <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
@@ -15,20 +15,30 @@
 #if $param_in:
   -in $param_in
 #end if
-#if $param_in_target:
-  -in_target $param_in_target
-#end if
-#if $param_in_decoy:
-  -in_decoy $param_in_decoy
-#end if
 #if $param_out:
   -out $param_out
 #end if
-#if $param_proteins_only:
-  -proteins_only
+#if $param_PSM:
+  -PSM
+  #if " " in str($param_PSM):
+    "$param_PSM"
+  #else
+    $param_PSM
+  #end if
 #end if
-#if $param_peptides_only:
-  -peptides_only
+#if $param_protein:
+  -protein
+  #if " " in str($param_protein):
+    "$param_protein"
+  #else
+    $param_protein
+  #end if
+#end if
+#if $param_FDR_PSM:
+  -FDR:PSM $param_FDR_PSM
+#end if
+#if $param_FDR_protein:
+  -FDR:protein $param_FDR_protein
 #end if
 #if $param_algorithm_no_qvalues:
   -algorithm:no_qvalues
@@ -52,11 +62,17 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="idxml" optional="True" label="Identification input file containing a search against a concatenated sequence database" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input"/>
-    <param name="param_in_target" type="data" format="idxml" optional="True" label="Identification input file containing a search against a target-only database" help="(-in_target) "/>
-    <param name="param_in_decoy" type="data" format="idxml" optional="True" label="Identification input file containing a search against a decoy-only database" help="(-in_decoy) "/>
-    <param name="param_proteins_only" display="radio" type="boolean" truevalue="-proteins_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on protein level is calculated" help="(-proteins_only) "/>
-    <param name="param_peptides_only" display="radio" type="boolean" truevalue="-peptides_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on peptide (PSM) level is calculated" help="(-peptides_only) "/>
+    <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/>
+    <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_FDR_PSM" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter PSMs based on q-value (" help="(-PSM) e.g., 0.05 = 5% FDR, disabled for 1)"/>
+    <param name="param_FDR_protein" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter proteins based on q-value (" help="(-protein) e.g., 0.05 = 5% FDR, disabled for 1)"/>
     <param name="param_algorithm_no_qvalues" display="radio" type="boolean" truevalue="-algorithm:no_qvalues" falsevalue="" checked="false" optional="True" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help="(-no_qvalues) "/>
     <param name="param_algorithm_use_all_hits" display="radio" type="boolean" truevalue="-algorithm:use_all_hits" falsevalue="" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits) "/>
     <param name="param_algorithm_split_charge_variants" display="radio" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" checked="false" optional="True" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help="(-split_charge_variants) "/>
diff -r a6a6a9a850b5 -r c221d1871982 macros.xml
--- a/macros.xml	Thu Apr 27 12:48:14 2017 -0400
+++ b/macros.xml	Fri Jul 14 18:43:05 2017 -0400
@@ -2,7 +2,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.1">openms</requirement>
+      <requirement type="package" version="2.2">openms</requirement>
       <requirement type="package" version="15.12.15.2">xtandem</requirement>
       <requirement type="package" version="1.0">fido</requirement>
       <requirement type="package" version="2016.10.26">msgf_plus</requirement>
diff -r a6a6a9a850b5 -r c221d1871982 readme.md
--- a/readme.md	Thu Apr 27 12:48:14 2017 -0400
+++ b/readme.md	Fri Jul 14 18:43:05 2017 -0400
@@ -14,15 +14,29 @@
 Generating OpenMS wrappers
 ==========================
 
- * install OpenMS (you can do this automatically through the Tool Shed)
+ * install OpenMS (you can do this automatically through Conda)
  * create a folder called CTD
- * inside of your new installed openms/bin folder, execute the following command:
+ * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
     
     ```bash
     for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
     ```
     
- * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
+ * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
+ 
+    ```bash
+    ls >> tools.txt
+    ```
+    
+ * search for the `bin` folder of your conda environment containing OpenMS and do:
+ 
+    ```bash
+    while read p; do
+        ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
+    done <tools.txt
+    ```
+    
+ * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
 
  * clone or install CTDopts
 
@@ -42,7 +56,7 @@
     git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository.
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
 
     ```bash
     python generator.py \ 
diff -r a6a6a9a850b5 -r c221d1871982 tool.conf
--- a/tool.conf	Thu Apr 27 12:48:14 2017 -0400
+++ b/tool.conf	Fri Jul 14 18:43:05 2017 -0400
@@ -6,13 +6,7 @@
     <tool file="openms/RTModel.xml"/>
     <tool file="openms/RTPredict.xml"/>
   </section>
-  <section id="section-id-DEFAULT" name="DEFAULT">
-    <tool file="openms/OpenSwathFileSplitter.xml"/>
-    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
-  </section>
   <section id="section-id-TargetedExperiments" name="Targeted Experiments">
-    <tool file="openms/ConvertTraMLToTSV.xml"/>
-    <tool file="openms/ConvertTSVToTraML.xml"/>
     <tool file="openms/InclusionExclusionListCreator.xml"/>
     <tool file="openms/MRMMapper.xml"/>
     <tool file="openms/OpenSwathAnalyzer.xml"/>
@@ -22,13 +16,17 @@
     <tool file="openms/OpenSwathDecoyGenerator.xml"/>
     <tool file="openms/OpenSwathDIAPreScoring.xml"/>
     <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
+    <tool file="openms/OpenSwathFileSplitter.xml"/>
+    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
     <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
     <tool file="openms/OpenSwathRTNormalizer.xml"/>
     <tool file="openms/PrecursorIonSelector.xml"/>
+    <tool file="openms/TargetedFileConverter.xml"/>
   </section>
   <section id="section-id-Utilities" name="Utilities">
     <tool file="openms/AccurateMassSearch.xml"/>
     <tool file="openms/CVInspector.xml"/>
+    <tool file="openms/DatabaseFilter.xml"/>
     <tool file="openms/DecoyDatabase.xml"/>
     <tool file="openms/DeMeanderize.xml"/>
     <tool file="openms/Digestor.xml"/>
@@ -44,7 +42,6 @@
     <tool file="openms/LabeledEval.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
-    <tool file="openms/MapAlignmentEvaluation.xml"/>
     <tool file="openms/MassCalculator.xml"/>
     <tool file="openms/MetaboliteSpectralMatcher.xml"/>
     <tool file="openms/MetaProSIP.xml"/>
@@ -62,12 +59,14 @@
     <tool file="openms/QCMerger.xml"/>
     <tool file="openms/QCShrinker.xml"/>
     <tool file="openms/RNPxl.xml"/>
+    <tool file="openms/RNPxlSearch.xml"/>
     <tool file="openms/RNPxlXICFilter.xml"/>
     <tool file="openms/RTEvaluation.xml"/>
     <tool file="openms/SemanticValidator.xml"/>
     <tool file="openms/SequenceCoverageCalculator.xml"/>
     <tool file="openms/SimpleSearchEngine.xml"/>
     <tool file="openms/SpecLibCreator.xml"/>
+    <tool file="openms/SpectraSTSearchAdapter.xml"/>
     <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
     <tool file="openms/TICCalculator.xml"/>
     <tool file="openms/TopPerc.xml"/>
@@ -78,6 +77,7 @@
     <tool file="openms/ConsensusMapNormalizer.xml"/>
     <tool file="openms/FeatureLinkerLabeled.xml"/>
     <tool file="openms/FeatureLinkerUnlabeled.xml"/>
+    <tool file="openms/FeatureLinkerUnlabeledKD.xml"/>
     <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
     <tool file="openms/MapRTTransformer.xml"/>
   </section>
@@ -154,9 +154,7 @@
     <tool file="openms/FeatureFinderMultiplex.xml"/>
     <tool file="openms/FeatureFinderSuperHirn.xml"/>
     <tool file="openms/IsobaricAnalyzer.xml"/>
-    <tool file="openms/ITRAQAnalyzer.xml"/>
     <tool file="openms/ProteinQuantifier.xml"/>
     <tool file="openms/ProteinResolver.xml"/>
-    <tool file="openms/TMTAnalyzer.xml"/>
   </section>
 </toolbox>