# HG changeset patch
# User galaxyp
# Date 1518458252 18000
# Node ID b09039836cb125c0f829f0a2ad7d7ee741d34b07
# Parent  c8b225c69a7fbb32e5a05a5b0d2bcf2e4087413f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r c8b225c69a7f -r b09039836cb1 SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 17:52:13 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-OMSSAAdapter
-MyriMatchAdapter
-PepNovoAdapter
-SeedListGenerator
-SpecLibSearcher
-MapAlignerIdentification
-MapAlignerPoseClustering
-MapAlignerSpectrum
-MapAlignerRTTransformer
diff -r c8b225c69a7f -r b09039836cb1 XTandemAdapter.xml
--- a/XTandemAdapter.xml	Thu Jan 11 17:52:13 2018 -0500
+++ b/XTandemAdapter.xml	Mon Feb 12 12:57:32 2018 -0500
@@ -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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Identification]-->
-<tool id="XTandemAdapter" name="XTandemAdapter" version="2.2.0.1">
+<tool id="XTandemAdapter" name="XTandemAdapter" version="2.3.0">
   <description>Annotates MS/MS spectra using X! Tandem.</description>
   <macros>
     <token name="@EXECUTABLE@">XTandemAdapter</token>
@@ -132,7 +132,7 @@
     </param>
     <param name="param_max_precursor_charge" type="integer" min="0" optional="True" value="4" label="Maximum precursor charge ('0' to use X! Tandem default)" help="(-max_precursor_charge) "/>
     <param name="param_no_isotope_error" display="radio" type="boolean" truevalue="-no_isotope_error" falsevalue="" checked="false" optional="True" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="(-no_isotope_error) Set this flag to disable"/>
-    <repeat name="rep_param_fixed_modifications" min="0"  title="param_fixed_modifications">
+    <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
       <param name="param_fixed_modifications" type="select" optional="True" label="Fixed modifications, specified using Unimod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5200,24 +5200,29 @@
     </repeat>
     <param name="param_minimum_fragment_mz" type="float" value="150.0" label="Minimum fragment mz" help="(-minimum_fragment_mz) "/>
     <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
-      <option value="CNBr">CNBr</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="Trypsin/P">Trypsin/P</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="Asp-N">Asp-N</option>
       <option value="Arg-C">Arg-C</option>
-      <option value="V8-E">V8-E</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="Lys-C">Lys-C</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="TrypChymo">TrypChymo</option>
       <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Asp-N/B">Asp-N/B</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="V8-E">V8-E</option>
     </param>
     <param name="param_missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help="(-missed_cleavages) "/>
     <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="Require only peptide end to have a valid cleavage site, not both" help="(-semi_cleavage) "/>
diff -r c8b225c69a7f -r b09039836cb1 macros.xml
--- a/macros.xml	Thu Jan 11 17:52:13 2018 -0500
+++ b/macros.xml	Mon Feb 12 12:57:32 2018 -0500
@@ -2,10 +2,10 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.2">openms</requirement>
+      <requirement type="package" version="2.3">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>
+      <requirement type="package" version="2017.07.21">msgf_plus</requirement>
       <yield/>
     </requirements>
   </xml>
diff -r c8b225c69a7f -r b09039836cb1 readme.md
--- a/readme.md	Thu Jan 11 17:52:13 2018 -0500
+++ b/readme.md	Mon Feb 12 12:57:32 2018 -0500
@@ -53,29 +53,29 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTDConverter.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. You might have to install `libxslt` and `lxml` to run it.
+ * If you have CTDopts and CTDConverter 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. Further information can be found on the CTDConverter page.
 
     ```bash
-    python generator.py \ 
+    python convert.py galaxy \ 
     -i /PATH/TO/YOUR/CTD/*.ctd \
     -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
     -d datatypes_conf.xml -g openms \
     -b version log debug test no_progress threads \
      in_type executable myrimatch_executable \
      fido_executable fidocp_executable \
-     omssa_executable pepnovo_executable \
+     omssa_executable pepnovo_e xecutable \
      xtandem_executable param_model_directory \
      java_executable java_memory java_permgen \
      r_executable rt_concat_trafo_out param_id_pool \
     -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
-    -s PATH/TO/SKIP_TOOLS_FILES.txt
+    -s PATH/TO/tools_blacklist.txt
     ```
 
 
- * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
+ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist:
 
     ```
     sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
@@ -171,8 +171,8 @@
     ```
     
 
- * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
-   by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
+ * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
+   by the automatic conversion step and are therefore in `tools_blacklist.txt`:
     * SeedListGenerator
     * SpecLibSearcher
     * MapAlignerIdentification
diff -r c8b225c69a7f -r b09039836cb1 tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 12:57:32 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer