Mercurial > repos > galaxyp > openms_mssimulator

diff MSSimulator.xml @ 11:04228172e123 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:12:16 +0000
parents 98bb49e7b5ba
children 9e6a371d539b
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--- a/MSSimulator.xml	Thu Sep 24 12:10:06 2020 +0000
+++ b/MSSimulator.xml	Tue Oct 13 20:12:16 2020 +0000
@@ -115,27 +115,21 @@
       <section name="MSSim" title="" help="" expanded="false">
         <section name="Digestion" title="" help="" expanded="false">
           <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="false" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="">
-            <option value="PepsinA">PepsinA</option>
-            <option value="TrypChymo">TrypChymo</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="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="Asp-N/B">Asp-N/B</option>
             <option value="Asp-N_ambic">Asp-N_ambic</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="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="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="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>
@@ -143,10 +137,16 @@
             <option value="PepsinA + P">PepsinA + P</option>
             <option value="cyanogen-bromide">cyanogen-bromide</option>
             <option value="Clostripain/P">Clostripain/P</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="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</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="no cleavage">no cleavage</option>
+            <option value="unspecific cleavage">unspecific cleavage</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" selected="true">Trypsin</option>
             <expand macro="list_string_san"/>
           </param>
@@ -510,19 +510,19 @@
       </section>
     </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="false">
-      <option value="out_FLAG">out (Controls the 'technical' randomness of the generated data)</option>
-      <option value="out_pm_FLAG">out_pm (Controls the 'technical' randomness of the generated data)</option>
-      <option value="out_fm_FLAG">out_fm (Controls the 'technical' randomness of the generated data)</option>
-      <option value="out_cm_FLAG">out_cm (Controls the 'technical' randomness of the generated data)</option>
-      <option value="out_lcm_FLAG">out_lcm (Controls the 'technical' randomness of the generated data)</option>
-      <option value="out_cntm_FLAG">out_cntm (Controls the 'technical' randomness of the generated data)</option>
-      <option value="out_id_FLAG">out_id (Controls the 'technical' randomness of the generated data)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_FLAG">out (output: simulated MS raw (profile) data)</option>
+      <option value="out_pm_FLAG">out_pm (output: ground-truth picked (centroided) MS data)</option>
+      <option value="out_fm_FLAG">out_fm (output: ground-truth features)</option>
+      <option value="out_cm_FLAG">out_cm (output: ground-truth features, grouping ESI charge variants of each parent peptide)</option>
+      <option value="out_lcm_FLAG">out_lcm (output: ground-truth features, grouping labeled variants)</option>
+      <option value="out_cntm_FLAG">out_cntm (output: ground-truth features caused by contaminants)</option>
+      <option value="out_id_FLAG">out_id (output: ground-truth MS2 peptide identifications)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -562,6 +562,6 @@
   <help><![CDATA[A highly configurable simulator for mass spectrometry experiments.
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_MSSimulator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSSimulator.html]]></help>
   <expand macro="references"/>
 </tool>