Mercurial > repos > galaxyp > openms_digestormotif

diff DigestorMotif.xml @ 13:3138bbc00588 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:43:43 +0000
parents 01f5e95b5961
children
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--- a/DigestorMotif.xml	Thu Dec 01 19:22:51 2022 +0000
+++ b/DigestorMotif.xml	Fri Jun 14 21:43:43 2024 +0000
@@ -1,6 +1,5 @@
-<?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 CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>digests a protein database in-silico</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,53 +38,53 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
-    <param argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/>
-    <param argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/>
-    <param argument="-out_option" type="integer" optional="true" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-      <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="Arg-C">Arg-C</option>
+    <param argument="-in" type="data" format="fasta" label="FASTA input file" help=" select fasta data sets(s)"/>
+    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
+    <param argument="-mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help=""/>
+    <param argument="-min_length" type="integer" value="6" label="minimum length of peptide" help=""/>
+    <param argument="-out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/>
+    <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+      <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="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</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="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="Asp-N_ambic">Asp-N_ambic</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="Trypsin" selected="true">Trypsin</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="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="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="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help="">
+    <param argument="-motif" type="text" value="M" label="the motif for the restricted peptidome" help="">
       <expand macro="list_string_san" name="motif"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -103,6 +102,6 @@
   <help><![CDATA[digests a protein database in-silico
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DigestorMotif.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DigestorMotif.html]]></help>
   <expand macro="references"/>
 </tool>