Mercurial > repos > galaxyp > openms_idfilter

diff IDFilter.xml @ 12:8d04dd993653 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
author galaxyp
date Thu, 24 Sep 2020 09:00:23 +0000
parents a050a685eea1
children 406612b1a8f1
line wrap: on
line diff
--- a/IDFilter.xml	Thu Sep 03 16:15:58 2020 +0000
+++ b/IDFilter.xml	Thu Sep 24 09:00:23 2020 +0000
@@ -5360,21 +5360,16 @@
     <section name="in_silico_digestion" title="This filter option removes peptide hits which are not in the list of in silico peptides generated by the rules specified below" help="" expanded="false">
       <param name="fasta" argument="-in_silico_digestion:fasta" type="data" format="fasta" optional="true" label="fasta protein sequence database" help=" select fasta data sets(s)"/>
       <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" optional="false" label="enzyme used for the digestion of the sample" help="">
+        <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>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</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="Formic_acid">Formic_acid</option>
+        <option value="Lys-C">Lys-C</option>
         <option value="Chymotrypsin">Chymotrypsin</option>
         <option value="Chymotrypsin/P">Chymotrypsin/P</option>
         <option value="CNBr">CNBr</option>
-        <option value="Arg-C/P">Arg-C/P</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>
@@ -5382,17 +5377,22 @@
         <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="Asp-N">Asp-N</option>
-        <option value="Arg-C">Arg-C</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="Asp-N">Asp-N</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</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>
         <expand macro="list_string_san"/>
       </param>
       <param name="specificity" argument="-in_silico_digestion:specificity" display="radio" type="select" optional="false" label="Specificity of the filte" help="">
@@ -5409,21 +5409,16 @@
         <expand macro="list_string_san"/>
       </param>
       <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" optional="false" label="enzyme used for the digestion of the sample" help="">
+        <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>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</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="Formic_acid">Formic_acid</option>
+        <option value="Lys-C">Lys-C</option>
         <option value="Chymotrypsin">Chymotrypsin</option>
         <option value="Chymotrypsin/P">Chymotrypsin/P</option>
         <option value="CNBr">CNBr</option>
-        <option value="Arg-C/P">Arg-C/P</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>
@@ -5431,17 +5426,22 @@
         <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="Asp-N">Asp-N</option>
-        <option value="Arg-C">Arg-C</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="Asp-N">Asp-N</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</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>
         <expand macro="list_string_san"/>
       </param>
     </section>