Mercurial > repos > galaxyp > openms_simplesearchengine

diff SimpleSearchEngine.xml @ 5:242ba7640825 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:54:18 -0500
parents 6ae859b4f243
children 3cec90deb64b
line wrap: on
line diff
--- a/SimpleSearchEngine.xml	Thu Jan 11 18:00:11 2018 -0500
+++ b/SimpleSearchEngine.xml	Mon Feb 12 12:54:18 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="2.2.0">
+<tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="2.3.0">
   <description>Annotates MS/MS spectra using SimpleSearchEngine.</description>
   <macros>
     <token name="@EXECUTABLE@">SimpleSearchEngine</token>
@@ -40,6 +40,17 @@
     $param_precursor_mass_tolerance_unit
   #end if
 #end if
+
+#if $rep_param_precursor_isotopes:
+-precursor:isotopes
+  #for token in $rep_param_precursor_isotopes:
+    #if " " in str(token):
+      "$token.param_precursor_isotopes"
+    #else
+      $token.param_precursor_isotopes
+    #end if
+  #end for
+#end if
 #if $param_fragment_mass_tolerance:
   -fragment:mass_tolerance $param_fragment_mass_tolerance
 #end if
@@ -104,38 +115,53 @@
     <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/>
     <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
-      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="V8-E">V8-E</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="PepsinA">PepsinA</option>
       <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="no cleavage">no cleavage</option>
       <option value="Arg-C">Arg-C</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="TrypChymo">TrypChymo</option>
+      <option value="CNBr">CNBr</option>
       <option value="V8-DE">V8-DE</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="V8-E">V8-E</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="Lys-C">Lys-C</option>
     </param>
     <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help="(-mass_tolerance) "/>
     <param name="param_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mass_tolerance_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
+    <repeat name="rep_param_precursor_isotopes" min="0" max="1" title="param_precursor_isotopes">
+      <param name="param_precursor_isotopes" type="text" size="30" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(-isotopes) (E.g.: 1 = prec. may be misassigned to first isotopic peak)">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help="(-mass_tolerance) "/>
     <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
-    <repeat name="rep_param_modifications_fixed" min="0" max="1" title="param_modifications_fixed">
+    <repeat name="rep_param_modifications_fixed" min="0" title="param_modifications_fixed">
       <param name="param_modifications_fixed" type="select" optional="True" label="Fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed) e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2668,7 +2694,7 @@
         <option value="trifluoro (L)">trifluoro (L)</option>
       </param>
     </repeat>
-    <repeat name="rep_param_modifications_variable" min="0" max="1" title="param_modifications_variable">
+    <repeat name="rep_param_modifications_variable" min="0" title="param_modifications_variable">
       <param name="param_modifications_variable" type="select" optional="True" label="Variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable) e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5218,5 +5244,5 @@
   <help>Annotates MS/MS spectra using SimpleSearchEngine.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/classSimpleSearchEngine.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SimpleSearchEngine.html</help>
 </tool>