# HG changeset patch
# User galaxyp
# Date 1518464027 18000
# Node ID de2ef1ec30d2b8fb3555d07714908cb554f349a8
# Parent  90754d1433b56304284e46edc7e5c5497aa178a0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r 90754d1433b5 -r de2ef1ec30d2 FileFilter.xml
--- a/FileFilter.xml	Mon Feb 12 08:34:56 2018 -0500
+++ b/FileFilter.xml	Mon Feb 12 14:33:47 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: [File Handling]-->
-<tool id="FileFilter" name="FileFilter" version="2.2.0">
+<tool id="FileFilter" name="FileFilter" version="2.3.0">
   <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
   <macros>
     <token name="@EXECUTABLE@">FileFilter</token>
@@ -373,7 +373,7 @@
     </param>
     <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/>
     <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/>
-    <repeat name="rep_param_peak_options_rm_pc_charge" min="0" max="1" title="param_peak_options_rm_pc_charge">
+    <repeat name="rep_param_peak_options_rm_pc_charge" min="0" title="param_peak_options_rm_pc_charge">
       <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!">
         <sanitizer>
           <valid initial="string.printable">
@@ -391,7 +391,7 @@
         </valid>
       </sanitizer>
     </param>
-    <repeat name="rep_param_peak_options_pc_mz_list" min="0" max="1" title="param_peak_options_pc_mz_list">
+    <repeat name="rep_param_peak_options_pc_mz_list" min="0" title="param_peak_options_pc_mz_list">
       <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept">
         <sanitizer>
           <valid initial="string.printable">
@@ -454,7 +454,7 @@
       <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
       <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
       <option value="Emission">Emission</option>
-      <option value="Absorbtion">Absorbtion</option>
+      <option value="Absorption">Absorption</option>
     </param>
     <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) ">
       <option value="Collision-induced dissociation">Collision-induced dissociation</option>
@@ -503,7 +503,7 @@
       <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
       <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
       <option value="Emission">Emission</option>
-      <option value="Absorbtion">Absorbtion</option>
+      <option value="Absorption">Absorption</option>
     </param>
     <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) ">
       <option value="Collision-induced dissociation">Collision-induced dissociation</option>
@@ -549,7 +549,7 @@
         </valid>
       </sanitizer>
     </param>
-    <repeat name="rep_param_consensus_map" min="0" max="1" title="param_consensus_map">
+    <repeat name="rep_param_consensus_map" min="0" title="param_consensus_map">
       <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) ">
         <sanitizer>
           <valid initial="string.printable">
@@ -565,7 +565,7 @@
       <option value="true" selected="true">true</option>
     </param>
     <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) &lt;br&gt;If consensus:blackorwhitelist:maps is specified, only these will be used. &lt;br&gt;"/>
-    <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" max="1" title="param_consensus_blackorwhitelist_maps">
+    <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" title="param_consensus_blackorwhitelist_maps">
       <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) ">
         <sanitizer>
           <valid initial="string.printable">
@@ -594,7 +594,7 @@
         </valid>
       </sanitizer>
     </param>
-    <repeat name="rep_param_f_and_c_remove_meta" min="0" max="1" title="param_f_and_c_remove_meta">
+    <repeat name="rep_param_f_and_c_remove_meta" min="0" title="param_f_and_c_remove_meta">
       <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!">
         <sanitizer>
           <valid initial="string.printable">
@@ -605,7 +605,7 @@
       </param>
     </repeat>
     <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/>
-    <repeat name="rep_param_id_sequences_whitelist" min="0" max="1" title="param_id_sequences_whitelist">
+    <repeat name="rep_param_id_sequences_whitelist" min="0" title="param_id_sequences_whitelist">
       <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)">
         <sanitizer>
           <valid initial="string.printable">
@@ -615,7 +615,7 @@
         </sanitizer>
       </param>
     </repeat>
-    <repeat name="rep_param_id_accessions_whitelist" min="0" max="1" title="param_id_accessions_whitelist">
+    <repeat name="rep_param_id_accessions_whitelist" min="0" title="param_id_accessions_whitelist">
       <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN">
         <sanitizer>
           <valid initial="string.printable">
diff -r 90754d1433b5 -r de2ef1ec30d2 SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Mon Feb 12 08:34:56 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 90754d1433b5 -r de2ef1ec30d2 macros.xml
--- a/macros.xml	Mon Feb 12 08:34:56 2018 -0500
+++ b/macros.xml	Mon Feb 12 14:33:47 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 90754d1433b5 -r de2ef1ec30d2 readme.md
--- a/readme.md	Mon Feb 12 08:34:56 2018 -0500
+++ b/readme.md	Mon Feb 12 14:33:47 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 90754d1433b5 -r de2ef1ec30d2 tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 14:33:47 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer