diff MSFraggerAdapter.xml @ 2:6bcc338b9dc6 draft

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

--- a/MSFraggerAdapter.xml	Wed Sep 23 15:01:51 2020 +0000
+++ b/MSFraggerAdapter.xml	Tue Oct 13 20:09:43 2020 +0000
@@ -89,25 +89,31 @@
     </section>
     <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false">
       <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="false" label="Name of the enzyme to be written to the pepXML file" help="">
+        <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>
         <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="unspecific cleavage">unspecific cleavage</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="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="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="Lys-C/P">Lys-C/P</option>
-        <option value="PepsinA">PepsinA</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>
@@ -115,12 +121,6 @@
         <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="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="Trypsin" selected="true">Trypsin</option>
         <expand macro="list_string_san"/>
       </param>
@@ -226,13 +226,13 @@
       <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <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">
-      <option value="opt_out_FLAG">opt_out (Statically add mass to tryptophan)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="opt_out_FLAG">opt_out (MSFragger optional output file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -250,6 +250,8 @@
     <expand macro="manutest_MSFraggerAdapter"/>
   </tests>
   <help><![CDATA[Peptide Identification with MSFragger
-]]></help>
+
+
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSFraggerAdapter.html]]></help>
   <expand macro="references"/>
 </tool>