# HG changeset patch
# User galaxyp
# Date 1518459143 18000
# Node ID 3822d4b3c74d8a2f1c22e553b2c5d8bb434ced53
# Parent  14a0112f07051ee0a8104685b6408f2f25de44cc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r 14a0112f0705 -r 3822d4b3c74d RNPxlSearch.xml
--- a/RNPxlSearch.xml	Thu Jan 11 18:03:03 2018 -0500
+++ b/RNPxlSearch.xml	Mon Feb 12 13:12:23 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: [Utilities]-->
-<tool id="RNPxlSearch" name="RNPxlSearch" version="2.2.0">
+<tool id="RNPxlSearch" name="RNPxlSearch" version="2.3.0">
   <description>Annotate RNA to peptide crosslinks in MS/MS spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">RNPxlSearch</token>
@@ -41,6 +41,17 @@
 #if $param_precursor_max_charge:
   -precursor:max_charge $param_precursor_max_charge
 #end if
+
+#if $rep_param_precursor_isotopes:
+-precursor:isotopes
+  #for token in $rep_param_precursor_isotopes:
+    #if " " in str(token):
+      "$token.param_precursor_isotopes"
+    #else
+      $token.param_precursor_isotopes
+    #end if
+  #end for
+#end if
 #if $param_fragment_mass_tolerance:
   -fragment:mass_tolerance $param_fragment_mass_tolerance
 #end if
@@ -189,12 +200,22 @@
     </param>
     <param name="param_precursor_min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help="(-min_charge) "/>
     <param name="param_precursor_max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help="(-max_charge) "/>
+    <repeat name="rep_param_precursor_isotopes" min="0" max="1" title="param_precursor_isotopes">
+      <param name="param_precursor_isotopes" type="text" size="30" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(-isotopes) (E.g.: 1 = prec. may be misassigned to first isotopic peak)">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help="(-mass_tolerance) "/>
     <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
-    <repeat name="rep_param_modifications_fixed" min="0" max="1" title="param_modifications_fixed">
+    <repeat name="rep_param_modifications_fixed" min="0" title="param_modifications_fixed">
       <param name="param_modifications_fixed" type="select" optional="True" label="Fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed) e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2727,7 +2748,7 @@
         <option value="trifluoro (L)">trifluoro (L)</option>
       </param>
     </repeat>
-    <repeat name="rep_param_modifications_variable" min="0" max="1" title="param_modifications_variable">
+    <repeat name="rep_param_modifications_variable" min="0" title="param_modifications_variable">
       <param name="param_modifications_variable" type="select" optional="True" label="Variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable) e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5263,26 +5284,31 @@
     <param name="param_modifications_variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help="(-variable_max_per_peptide) "/>
     <param name="param_peptide_missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help="(-missed_cleavages) "/>
     <param name="param_peptide_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
-      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Lys-N">Lys-N</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="V8-DE">V8-DE</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="Lys-C">Lys-C</option>
-      <option value="V8-E">V8-E</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
       <option value="no cleavage">no cleavage</option>
-      <option value="CNBr">CNBr</option>
+      <option value="Arg-C/P">Arg-C/P</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
       <option value="Arg-C">Arg-C</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="V8-E">V8-E</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
     </param>
     <param name="param_RNPxl_length" type="integer" value="2" label="Oligonucleotide maximum length" help="(-length) 0 = disable search for RNA variants"/>
     <param name="param_RNPxl_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)">
@@ -5362,5 +5388,5 @@
   <help>Annotate RNA to peptide crosslinks in MS/MS spectra.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/develop-documentation/html/classRNPxlSearch.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlSearch.html</help>
 </tool>
diff -r 14a0112f0705 -r 3822d4b3c74d SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 18:03:03 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 14a0112f0705 -r 3822d4b3c74d macros.xml
--- a/macros.xml	Thu Jan 11 18:03:03 2018 -0500
+++ b/macros.xml	Mon Feb 12 13:12:23 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 14a0112f0705 -r 3822d4b3c74d readme.md
--- a/readme.md	Thu Jan 11 18:03:03 2018 -0500
+++ b/readme.md	Mon Feb 12 13:12:23 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 14a0112f0705 -r 3822d4b3c74d tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 13:12:23 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer