# HG changeset patch
# User galaxyp
# Date 1502287176 14400
# Node ID a4c3db6825f4eb6ed4d4a1febc0ec123adc70787
# Parent  7c2b85eb3ccf3f532fe3cb27414f7fad77fe4864
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

diff -r 7c2b85eb3ccf -r a4c3db6825f4 MSSimulator.xml
--- a/MSSimulator.xml	Wed Mar 01 12:59:29 2017 -0500
+++ b/MSSimulator.xml	Wed Aug 09 09:59:36 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>
@@ -38,10 +38,20 @@
   -out_id $param_out_id
 #end if
 #if $param_algorithm_MSSim_Digestion_enzyme:
-  -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme
+  -algorithm:MSSim:Digestion:enzyme
+  #if " " in str($param_algorithm_MSSim_Digestion_enzyme):
+    "$param_algorithm_MSSim_Digestion_enzyme"
+  #else
+    $param_algorithm_MSSim_Digestion_enzyme
+  #end if
 #end if
 #if $param_algorithm_MSSim_Digestion_model:
-  -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model
+  -algorithm:MSSim:Digestion:model
+  #if " " in str($param_algorithm_MSSim_Digestion_model):
+    "$param_algorithm_MSSim_Digestion_model"
+  #else
+    $param_algorithm_MSSim_Digestion_model
+  #end if
 #end if
 #if $param_algorithm_MSSim_Digestion_min_peptide_length:
   -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
@@ -53,10 +63,20 @@
   -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
 #end if
 #if $param_algorithm_MSSim_RT_rt_column:
-  -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column
+  -algorithm:MSSim:RT:rt_column
+  #if " " in str($param_algorithm_MSSim_RT_rt_column):
+    "$param_algorithm_MSSim_RT_rt_column"
+  #else
+    $param_algorithm_MSSim_RT_rt_column
+  #end if
 #end if
 #if $param_algorithm_MSSim_RT_auto_scale:
-  -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale
+  -algorithm:MSSim:RT:auto_scale
+  #if " " in str($param_algorithm_MSSim_RT_auto_scale):
+    "$param_algorithm_MSSim_RT_auto_scale"
+  #else
+    $param_algorithm_MSSim_RT_auto_scale
+  #end if
 #end if
 #if $param_algorithm_MSSim_RT_total_gradient_time:
   -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
@@ -167,16 +187,31 @@
   -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit
 #end if
 #if $param_algorithm_MSSim_RawSignal_enabled:
-  -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled
+  -algorithm:MSSim:RawSignal:enabled
+  #if " " in str($param_algorithm_MSSim_RawSignal_enabled):
+    "$param_algorithm_MSSim_RawSignal_enabled"
+  #else
+    $param_algorithm_MSSim_RawSignal_enabled
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawSignal_peak_shape:
-  -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape
+  -algorithm:MSSim:RawSignal:peak_shape
+  #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape):
+    "$param_algorithm_MSSim_RawSignal_peak_shape"
+  #else
+    $param_algorithm_MSSim_RawSignal_peak_shape
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawSignal_resolution_value:
   -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
 #end if
 #if $param_algorithm_MSSim_RawSignal_resolution_type:
-  -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type
+  -algorithm:MSSim:RawSignal:resolution:type
+  #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type):
+    "$param_algorithm_MSSim_RawSignal_resolution_type"
+  #else
+    $param_algorithm_MSSim_RawSignal_resolution_type
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawSignal_baseline_scaling:
   -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
@@ -221,7 +256,12 @@
   -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_status:
-  -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status
+  -algorithm:MSSim:RawTandemSignal:status
+  #if " " in str($param_algorithm_MSSim_RawTandemSignal_status):
+    "$param_algorithm_MSSim_RawTandemSignal_status"
+  #else
+    $param_algorithm_MSSim_RawTandemSignal_status
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
   -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
@@ -312,6 +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
@@ -319,10 +362,20 @@
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
-  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
+  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions
+  #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions):
+    "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions"
+  #else
+    $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
-  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
+  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions
+  #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions):
+    "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions"
+  #else
+    $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
@@ -427,16 +480,31 @@
   -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity
 #end if
 #if $param_algorithm_MSSim_Global_ionization_type:
-  -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type
+  -algorithm:MSSim:Global:ionization_type
+  #if " " in str($param_algorithm_MSSim_Global_ionization_type):
+    "$param_algorithm_MSSim_Global_ionization_type"
+  #else
+    $param_algorithm_MSSim_Global_ionization_type
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_type:
-  -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type
+  -algorithm:MSSim:Labeling:type
+  #if " " in str($param_algorithm_MSSim_Labeling_type):
+    "$param_algorithm_MSSim_Labeling_type"
+  #else
+    $param_algorithm_MSSim_Labeling_type
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift:
   -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
 #end if
 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
-  -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins
+  -algorithm:MSSim:Labeling:ICPL:label_proteins
+  #if " " in str($param_algorithm_MSSim_Labeling_ICPL_label_proteins):
+    "$param_algorithm_MSSim_Labeling_ICPL_label_proteins"
+  #else
+    $param_algorithm_MSSim_Labeling_ICPL_label_proteins
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
   -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
@@ -454,7 +522,12 @@
   -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine     "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine"
 #end if
 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
-  -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ
+  -algorithm:MSSim:Labeling:itraq:iTRAQ
+  #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ):
+    "$param_algorithm_MSSim_Labeling_itraq_iTRAQ"
+  #else
+    $param_algorithm_MSSim_Labeling_itraq_iTRAQ
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift:
   -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
@@ -488,10 +561,20 @@
   -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
 #end if
 #if $param_algorithm_RandomNumberGenerators_biological:
-  -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological
+  -algorithm:RandomNumberGenerators:biological
+  #if " " in str($param_algorithm_RandomNumberGenerators_biological):
+    "$param_algorithm_RandomNumberGenerators_biological"
+  #else
+    $param_algorithm_RandomNumberGenerators_biological
+  #end if
 #end if
 #if $param_algorithm_RandomNumberGenerators_technical:
-  -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical
+  -algorithm:RandomNumberGenerators:technical
+  #if " " in str($param_algorithm_RandomNumberGenerators_technical):
+    "$param_algorithm_RandomNumberGenerators_technical"
+  #else
+    $param_algorithm_RandomNumberGenerators_technical
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -543,26 +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>
@@ -747,6 +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 7c2b85eb3ccf -r a4c3db6825f4 datatypes_conf.xml
--- a/datatypes_conf.xml	Wed Mar 01 12:59:29 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<datatypes>
-  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
-    <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/>
-    <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/>
-    <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/>
-    <datatype extension="grid" type="galaxy.datatypes.data:Grid"/>
-    <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/>
-    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
-    <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-  </registration>
-</datatypes>
diff -r 7c2b85eb3ccf -r a4c3db6825f4 filetypes.txt
--- a/filetypes.txt	Wed Mar 01 12:59:29 2017 -0500
+++ b/filetypes.txt	Wed Aug 09 09:59:36 2017 -0400
@@ -14,7 +14,7 @@
 consensusXML  consensusxml      galaxy.datatypes.proteomics:ConsensusXML    application/xml
 edta          tabular           galaxy.datatypes.tabular:Tabular 
 featureXML    featurexml        galaxy.datatypes.proteomics:FeatureXML      application/xml
-idXML         idxml             galaxy.datatypes.proteomics:IdXM            application/xml
+idXML         idxml             galaxy.datatypes.proteomics:IdXML           application/xml
 mzML          mzml              galaxy.datatypes.proteomics:MzML            application/xml
 mzXML         mzxml             galaxy.datatypes.proteomics:MzXML           application/xml
 pepXML        pepxml            galaxy.datatypes.proteomics:PepXml          application/xml
@@ -26,4 +26,4 @@
 msp           msp               galaxy.datatypes.proteomics:Msp
 mzid          mzid              galaxy.datatypes.proteomics:MzIdentML       application/xml
 png           png               galaxy.datatypes.images:Png                 image/png
-mgf           mgf               galaxy.datatypes.proteomics:Mgf
\ No newline at end of file
+mgf           mgf               galaxy.datatypes.proteomics:Mgf
diff -r 7c2b85eb3ccf -r a4c3db6825f4 macros.xml
--- a/macros.xml	Wed Mar 01 12:59:29 2017 -0500
+++ b/macros.xml	Wed Aug 09 09:59:36 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 7c2b85eb3ccf -r a4c3db6825f4 readme.md
--- a/readme.md	Wed Mar 01 12:59:29 2017 -0500
+++ b/readme.md	Wed Aug 09 09:59:36 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
 
@@ -39,10 +53,10 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/blankclemens/CTD2Galaxy.git
+    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. 
+ * 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 \ 
@@ -102,17 +116,32 @@
     [...]
     ]]>
     ```
- * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
+    
+ * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
  
-        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
-     
-   and change it to
+   ```
+    <command><![CDATA[
    
-        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
+      ## check input file type
+      #set $in_type = $param_in.ext
+
+      ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+      ln -s '$param_in' 'param_in.${in_type}' &&
+
+      IDFileConverter
 
- * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
+      #if $param_in:
+        -in 'param_in.${in_type}'
+      #end if
+
+        [...]
+        ]]>
+    ```
+
+ * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
  
-        <data name="param_out" metadata_source="param_in" auto_format="true"/>
+   - `<data name="param_out" auto_format="true"/>`
+   - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
         
  * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.
  
diff -r 7c2b85eb3ccf -r a4c3db6825f4 tool.conf
--- a/tool.conf	Wed Mar 01 12:59:29 2017 -0500
+++ b/tool.conf	Wed Aug 09 09:59:36 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>