# HG changeset patch
# User galaxyp
# Date 1518458632 18000
# Node ID fc6ccd403439010f0bffa04f4e886809b2c3ca99
# Parent  e039cc5c7aed47c33db1445bcb614ca7053f9186
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r e039cc5c7aed -r fc6ccd403439 PeptideIndexer.xml
--- a/PeptideIndexer.xml	Thu Jan 11 18:07:21 2018 -0500
+++ b/PeptideIndexer.xml	Mon Feb 12 13:03:52 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: [ID Processing]-->
-<tool id="PeptideIndexer" name="PeptideIndexer" version="2.2.0">
+<tool id="PeptideIndexer" name="PeptideIndexer" version="2.3.0">
   <description>Refreshes the protein references for all peptide hits.</description>
   <macros>
     <token name="@EXECUTABLE@">PeptideIndexer</token>
@@ -119,25 +119,30 @@
     <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
     <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Formic_acid">Formic_acid</option>
       <option value="TrypChymo">TrypChymo</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Arg-C">Arg-C</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="V8-E">V8-E</option>
       <option value="PepsinA">PepsinA</option>
       <option value="Asp-N">Asp-N</option>
-      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Lys-C">Lys-C</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
       <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="V8-E">V8-E</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="V8-DE">V8-DE</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
     </param>
     <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt;  'full': both internal cleavage sites must match. &lt;br&gt;  'semi': one of two internal cleavage sites must match. &lt;br&gt;  'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
       <option value="full" selected="true">full</option>
diff -r e039cc5c7aed -r fc6ccd403439 SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 18:07:21 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 e039cc5c7aed -r fc6ccd403439 macros.xml
--- a/macros.xml	Thu Jan 11 18:07:21 2018 -0500
+++ b/macros.xml	Mon Feb 12 13:03:52 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 e039cc5c7aed -r fc6ccd403439 readme.md
--- a/readme.md	Thu Jan 11 18:07:21 2018 -0500
+++ b/readme.md	Mon Feb 12 13:03:52 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 e039cc5c7aed -r fc6ccd403439 tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 13:03:52 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer