diff DecoyDatabase.xml @ 13:71a6c870aa48 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

--- a/DecoyDatabase.xml	Wed Sep 23 15:02:35 2020 +0000
+++ b/DecoyDatabase.xml	Tue Oct 13 20:22:51 2020 +0000
@@ -62,16 +62,12 @@
       <expand macro="list_string_san"/>
     </param>
     <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Enzyme used for the digestion of the sample" help="Only applicable if parameter 'type' is 'protein'">
-      <option value="Asp-N">Asp-N</option>
-      <option value="Asp-N/B">Asp-N/B</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
       <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-      <option value="Glu-C+P">Glu-C+P</option>
-      <option value="PepsinA + P">PepsinA + P</option>
-      <option value="cyanogen-bromide">cyanogen-bromide</option>
-      <option value="Clostripain/P">Clostripain/P</option>
-      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
+      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Chymotrypsin/P">Chymotrypsin/P</option>
       <option value="CNBr">CNBr</option>
@@ -82,18 +78,22 @@
       <option value="PepsinA">PepsinA</option>
       <option value="TrypChymo">TrypChymo</option>
       <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+      <option value="Glu-C+P">Glu-C+P</option>
+      <option value="PepsinA + P">PepsinA + P</option>
+      <option value="cyanogen-bromide">cyanogen-bromide</option>
+      <option value="Clostripain/P">Clostripain/P</option>
+      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="no cleavage">no cleavage</option>
       <option value="V8-DE">V8-DE</option>
       <option value="V8-E">V8-E</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="Arg-C/P">Arg-C/P</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="iodosobenzoate">iodosobenzoate</option>
-      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
       <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san"/>
     </param>
@@ -110,12 +110,12 @@
       <param name="seed" argument="-seed" type="text" optional="true" value="1" label="Random number seed (use 'time' for system time)" help="">
         <expand macro="list_string_san"/>
       </param>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -132,6 +132,6 @@
   <help><![CDATA[Create decoy sequence database from forward sequence database.
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_DecoyDatabase.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DecoyDatabase.html]]></help>
   <expand macro="references"/>
 </tool>