# HG changeset patch
# User galaxyp
# Date 1500072964 14400
# Node ID fcbdc271f48cf88c468f8c1a7d72324b7195c387
# Parent  b8103b8deae20ff75d7fae8d3a649684e9e8da86
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

diff -r b8103b8deae2 -r fcbdc271f48c MSSimulator.xml
--- a/MSSimulator.xml	Thu Apr 27 12:58:04 2017 -0400
+++ b/MSSimulator.xml	Fri Jul 14 18:56:04 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: [Utilities]-->
-<tool id="MSSimulator" name="MSSimulator" version="2.1.0">
+<tool id="MSSimulator" name="MSSimulator" version="2.2.0">
   <description>A highly configurable simulator for mass spectrometry experiments.</description>
   <macros>
     <token name="@EXECUTABLE@">MSSimulator</token>
@@ -352,6 +352,9 @@
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
 #end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges:
+  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges
+#end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
 #end if
@@ -623,26 +626,26 @@
       </sanitizer>
     </param>
     <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) ">
-      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Asp-N">Asp-N</option>
       <option value="Lys-C">Lys-C</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
       <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="V8-E">V8-E</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
     </param>
     <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
       <option value="trained">trained</option>
@@ -827,6 +830,7 @@
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/>
+    <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" falsevalue="" checked="false" optional="True" label="Adds precursor peaks with all charges in the given range" help="(-add_all_precursor_charges) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) ">
diff -r b8103b8deae2 -r fcbdc271f48c macros.xml
--- a/macros.xml	Thu Apr 27 12:58:04 2017 -0400
+++ b/macros.xml	Fri Jul 14 18:56:04 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 b8103b8deae2 -r fcbdc271f48c readme.md
--- a/readme.md	Thu Apr 27 12:58:04 2017 -0400
+++ b/readme.md	Fri Jul 14 18:56:04 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 b8103b8deae2 -r fcbdc271f48c tool.conf
--- a/tool.conf	Thu Apr 27 12:58:04 2017 -0400
+++ b/tool.conf	Fri Jul 14 18:56:04 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>