# HG changeset patch
# User galaxyp
# Date 1518457994 18000
# Node ID edb972ad2c8114f231cb1d0315c5844e276a7960
# Parent  1dc75c2bf867b26ae10fc303458d50cf737e8ecd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r 1dc75c2bf867 -r edb972ad2c81 IsobaricAnalyzer.xml
--- a/IsobaricAnalyzer.xml	Thu Jan 11 17:43:42 2018 -0500
+++ b/IsobaricAnalyzer.xml	Mon Feb 12 12:53:14 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: [Quantitation]-->
-<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0">
+<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.3.0">
   <description>Calculates isobaric quantitative values for peptides</description>
   <macros>
     <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
@@ -184,6 +184,58 @@
     #end if
   #end for
 #end if
+#if $param_tmt11plex_channel_126_description:
+  -tmt11plex:channel_126_description     "$param_tmt11plex_channel_126_description"
+#end if
+#if $param_tmt11plex_channel_127N_description:
+  -tmt11plex:channel_127N_description     "$param_tmt11plex_channel_127N_description"
+#end if
+#if $param_tmt11plex_channel_127C_description:
+  -tmt11plex:channel_127C_description     "$param_tmt11plex_channel_127C_description"
+#end if
+#if $param_tmt11plex_channel_128N_description:
+  -tmt11plex:channel_128N_description     "$param_tmt11plex_channel_128N_description"
+#end if
+#if $param_tmt11plex_channel_128C_description:
+  -tmt11plex:channel_128C_description     "$param_tmt11plex_channel_128C_description"
+#end if
+#if $param_tmt11plex_channel_129N_description:
+  -tmt11plex:channel_129N_description     "$param_tmt11plex_channel_129N_description"
+#end if
+#if $param_tmt11plex_channel_129C_description:
+  -tmt11plex:channel_129C_description     "$param_tmt11plex_channel_129C_description"
+#end if
+#if $param_tmt11plex_channel_130N_description:
+  -tmt11plex:channel_130N_description     "$param_tmt11plex_channel_130N_description"
+#end if
+#if $param_tmt11plex_channel_130C_description:
+  -tmt11plex:channel_130C_description     "$param_tmt11plex_channel_130C_description"
+#end if
+#if $param_tmt11plex_channel_131N_description:
+  -tmt11plex:channel_131N_description     "$param_tmt11plex_channel_131N_description"
+#end if
+#if $param_tmt11plex_channel_131C_description:
+  -tmt11plex:channel_131C_description     "$param_tmt11plex_channel_131C_description"
+#end if
+#if $param_tmt11plex_reference_channel:
+  -tmt11plex:reference_channel
+  #if " " in str($param_tmt11plex_reference_channel):
+    "$param_tmt11plex_reference_channel"
+  #else
+    $param_tmt11plex_reference_channel
+  #end if
+#end if
+
+#if $rep_param_tmt11plex_correction_matrix:
+-tmt11plex:correction_matrix
+  #for token in $rep_param_tmt11plex_correction_matrix:
+    #if " " in str(token):
+      "$token.param_tmt11plex_correction_matrix"
+    #else
+      $token.param_tmt11plex_correction_matrix
+    #end if
+  #end for
+#end if
 #if $param_tmt6plex_channel_126_description:
   -tmt6plex:channel_126_description     "$param_tmt6plex_channel_126_description"
 #end if
@@ -234,14 +286,15 @@
 #end if
 </command>
   <inputs>
-    <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
+    <param name="param_type" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
       <option value="itraq4plex" selected="true">itraq4plex</option>
       <option value="itraq8plex">itraq8plex</option>
       <option value="tmt10plex">tmt10plex</option>
+      <option value="tmt11plex">tmt11plex</option>
       <option value="tmt6plex">tmt6plex</option>
     </param>
     <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
-    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/mount/miniconda3/envs/openms2.2/share/OpenMS/IDPool/IDPool.txt)">
+    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use share/OpenMS/IDPool/IDPool.txt)">
       <sanitizer>
         <valid initial="string.printable">
           <remove value="'"/>
@@ -498,6 +551,117 @@
         </sanitizer>
       </param>
     </repeat>
+    <param name="param_tmt11plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_131N_description" type="text" size="30" label="Description for the content of the 131N channel" help="(-channel_131N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_131C_description" type="text" size="30" label="Description for the content of the 131C channel" help="(-channel_131C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="(-reference_channel) ">
+      <option value="126" selected="true">126</option>
+      <option value="127N">127N</option>
+      <option value="127C">127C</option>
+      <option value="128N">128N</option>
+      <option value="128C">128C</option>
+      <option value="129N">129N</option>
+      <option value="129C">129C</option>
+      <option value="130N">130N</option>
+      <option value="130C">130C</option>
+      <option value="131N">131N</option>
+      <option value="131C">131C</option>
+    </param>
+    <repeat name="rep_param_tmt11plex_correction_matrix" min="0" max="1" title="param_tmt11plex_correction_matrix">
+      <param name="param_tmt11plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_tmt6plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
       <sanitizer>
         <valid initial="string.printable">
diff -r 1dc75c2bf867 -r edb972ad2c81 SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 17:43:42 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 1dc75c2bf867 -r edb972ad2c81 macros.xml
--- a/macros.xml	Thu Jan 11 17:43:42 2018 -0500
+++ b/macros.xml	Mon Feb 12 12:53:14 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 1dc75c2bf867 -r edb972ad2c81 readme.md
--- a/readme.md	Thu Jan 11 17:43:42 2018 -0500
+++ b/readme.md	Mon Feb 12 12:53:14 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 1dc75c2bf867 -r edb972ad2c81 tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 12:53:14 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer