# HG changeset patch
# User galaxyp
# Date 1518458989 18000
# Node ID 3d5cda05df459c950dee8a3cc018fa13eedb8580
# Parent  27cba4c5fc4260650c46c2f3e110ded109dcf568
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r 27cba4c5fc42 -r 3d5cda05df45 FileMerger.xml
--- a/FileMerger.xml	Thu Jan 11 17:45:16 2018 -0500
+++ b/FileMerger.xml	Mon Feb 12 13:09:49 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="FileMerger" name="FileMerger" version="2.2.0">
+<tool id="FileMerger" name="FileMerger" version="2.3.0">
   <description>Merges several MS files into one file.</description>
   <macros>
     <token name="@EXECUTABLE@">FileMerger</token>
@@ -26,6 +26,16 @@
   -rt_concat:gap $param_rt_concat_gap
 #end if
 
+#if $rep_param_rt_concat_trafo_out:
+-rt_concat:trafo_out
+  #for token in $rep_param_rt_concat_trafo_out:
+    #if " " in str(token):
+      "$token.param_rt_concat_trafo_out"
+    #else
+      $token.param_rt_concat_trafo_out
+    #end if
+  #end for
+#end if
 #if $param_raw_rt_auto:
   -raw:rt_auto
 #end if
@@ -53,7 +63,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
+    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml,fasta" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
       <sanitizer>
         <valid initial="string.printable">
           <remove value="'"/>
@@ -65,7 +75,7 @@
     <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
     <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
     <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
-      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="Custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
+      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
         <sanitizer>
           <valid initial="string.printable">
             <remove value="'"/>
@@ -81,7 +91,8 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="mzml"/>
+    <data name="param_out" format="featurexml"/>
+    <data name="param_rt_concat_trafo_out" format="trafoxml"/>
   </outputs>
   <help>Merges several MS files into one file.
 
diff -r 27cba4c5fc42 -r 3d5cda05df45 SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 17:45:16 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 27cba4c5fc42 -r 3d5cda05df45 macros.xml
--- a/macros.xml	Thu Jan 11 17:45:16 2018 -0500
+++ b/macros.xml	Mon Feb 12 13:09:49 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 27cba4c5fc42 -r 3d5cda05df45 readme.md
--- a/readme.md	Thu Jan 11 17:45:16 2018 -0500
+++ b/readme.md	Mon Feb 12 13:09:49 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 27cba4c5fc42 -r 3d5cda05df45 tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 13:09:49 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer