# HG changeset patch
# User galaxyp
# Date 1518459274 18000
# Node ID a7ef3b2f3621e0e5115f47e41a19c283085b0260
# Parent  252ef1ffd08d1922e39c41a41842f17651ca6225
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r 252ef1ffd08d -r a7ef3b2f3621 AccurateMassSearch.xml
--- a/AccurateMassSearch.xml	Thu Jan 11 17:46:10 2018 -0500
+++ b/AccurateMassSearch.xml	Mon Feb 12 13:14:34 2018 -0500
@@ -1,8 +1,8 @@
 <?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="AccurateMassSearch" name="AccurateMassSearch" version="2.2.0">
-  <description>Find potential HMDB ids within the given mass error window.</description>
+<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.3.0">
+  <description>Match MS signals to molecules from a database by mass.</description>
   <macros>
     <token name="@EXECUTABLE@">AccurateMassSearch</token>
     <import>macros.xml</import>
@@ -21,11 +21,11 @@
 #if $param_out_annotation:
   -out_annotation $param_out_annotation
 #end if
-#if $param_positive_adducts_file:
-  -positive_adducts_file $param_positive_adducts_file
+#if $param_positive_adducts:
+  -positive_adducts $param_positive_adducts
 #end if
-#if $param_negative_adducts_file:
-  -negative_adducts_file $param_negative_adducts_file
+#if $param_negative_adducts:
+  -negative_adducts $param_negative_adducts
 #end if
 -db:mapping
   #for token in $param_db_mapping:
@@ -71,8 +71,8 @@
 </command>
   <inputs>
     <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/>
-    <param name="param_positive_adducts_file" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts_file) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
-    <param name="param_negative_adducts_file" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts_file) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
+    <param name="param_positive_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
+    <param name="param_negative_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
     <param name="param_db_mapping" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="(-mapping) If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used">
       <sanitizer>
         <valid initial="string.printable">
@@ -110,7 +110,7 @@
     <data name="param_out" format="tabular"/>
     <data name="param_out_annotation" metadata_source="param_in" format="input"/>
   </outputs>
-  <help>Find potential HMDB ids within the given mass error window.
+  <help>Match MS signals to molecules from a database by mass.
 
 
 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
diff -r 252ef1ffd08d -r a7ef3b2f3621 SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 17:46:10 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 252ef1ffd08d -r a7ef3b2f3621 macros.xml
--- a/macros.xml	Thu Jan 11 17:46:10 2018 -0500
+++ b/macros.xml	Mon Feb 12 13:14:34 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 252ef1ffd08d -r a7ef3b2f3621 readme.md
--- a/readme.md	Thu Jan 11 17:46:10 2018 -0500
+++ b/readme.md	Mon Feb 12 13:14:34 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 252ef1ffd08d -r a7ef3b2f3621 tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 13:14:34 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer