diff CruxAdapter.xml @ 2:aed7aeb6feec draft

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

--- a/CruxAdapter.xml	Thu Sep 24 12:15:56 2020 +0000
+++ b/CruxAdapter.xml	Tue Oct 13 20:05:24 2020 +0000
@@ -71,22 +71,22 @@
     <param name="run_percolator" argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
     <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
       <option value="custom-enzyme">custom-enzyme</option>
+      <option value="arg-c">arg-c</option>
+      <option value="asp-n">asp-n</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
+      <option value="staph-protease">staph-protease</option>
+      <option value="proline-endopeptidase">proline-endopeptidase</option>
       <option value="glu-c">glu-c</option>
       <option value="pepsin-a">pepsin-a</option>
       <option value="cyanogen-bromide">cyanogen-bromide</option>
       <option value="clostripain">clostripain</option>
       <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-      <option value="arg-c">arg-c</option>
-      <option value="asp-n">asp-n</option>
       <option value="no-enzyme">no-enzyme</option>
-      <option value="iodosobenzoate">iodosobenzoate</option>
-      <option value="staph-protease">staph-protease</option>
-      <option value="proline-endopeptidase">proline-endopeptidase</option>
+      <option value="chymotrypsin">chymotrypsin</option>
+      <option value="trypsin/p">trypsin/p</option>
       <option value="elastase">elastase</option>
-      <option value="chymotrypsin">chymotrypsin</option>
       <option value="lys-c">lys-c</option>
       <option value="lys-n">lys-n</option>
-      <option value="trypsin/p">trypsin/p</option>
       <option value="trypsin" selected="true">trypsin</option>
       <expand macro="list_string_san"/>
     </param>
@@ -97,14 +97,14 @@
       <expand macro="list_string_san"/>
     </param>
     <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
-    <param name="decoy_format" argument="-decoy-format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
+    <param name="decoy_format" argument="-decoy_format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
       <option value="none">none</option>
       <option value="shuffle" selected="true">shuffle</option>
       <option value="peptide-reverse">peptide-reverse</option>
       <option value="protein-reverse">protein-reverse</option>
       <expand macro="list_string_san"/>
     </param>
-    <param name="keep_terminal_aminos" argument="-keep-terminal-aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
+    <param name="keep_terminal_aminos" argument="-keep_terminal_aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
       <option value="N">N</option>
       <option value="C">C</option>
       <option value="NC" selected="true">NC</option>
@@ -131,12 +131,12 @@
       </param>
       <param name="deisotope" argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
       <param name="report_decoys" argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
-      <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>
@@ -153,6 +153,6 @@
   <help><![CDATA[Identifies MS/MS spectra using Crux.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_CruxAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CruxAdapter.html]]></help>
   <expand macro="references"/>
 </tool>