diff PeptideIndexer.xml @ 10:cb18120926b0 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"

--- a/PeptideIndexer.xml	Thu Sep 03 16:23:00 2020 +0000
+++ b/PeptideIndexer.xml	Thu Sep 24 09:55:34 2020 +0000
@@ -70,15 +70,13 @@
     <param name="IL_equivalent" argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
     <section name="enzyme" title="" help="" expanded="false">
       <param name="name" argument="-enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="CNBr">CNBr</option>
-        <option value="Formic_acid">Formic_acid</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</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="staphylococcal protease/D">staphylococcal protease/D</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>
@@ -86,22 +84,24 @@
         <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
         <option value="no cleavage">no cleavage</option>
         <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Formic_acid">Formic_acid</option>
+        <option value="Lys-C">Lys-C</option>
+        <option value="Lys-N">Lys-N</option>
+        <option value="Lys-C/P">Lys-C/P</option>
+        <option value="PepsinA">PepsinA</option>
         <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin/P">Trypsin/P</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="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="2-iodobenzoate">2-iodobenzoate</option>
         <option value="iodosobenzoate">iodosobenzoate</option>
-        <option value="Arg-C">Arg-C</option>
-        <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Lys-C">Lys-C</option>
-        <option value="Lys-N">Lys-N</option>
-        <option value="Lys-C/P">Lys-C/P</option>
-        <option value="PepsinA">PepsinA</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>