Mercurial > repos > galaxyp > openms_digestor

diff Digestor.xml @ 15:74db964d4818 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 21:36:14 +0000
parents 13399dc8f687
children
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--- a/Digestor.xml	Thu Dec 01 19:09:26 2022 +0000
+++ b/Digestor.xml	Fri Jun 14 21:36:14 2024 +0000
@@ -1,8 +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 CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Digests a protein database in-silico.</description>
+  <description>Digests a protein database in-silico</description>
   <macros>
     <token name="@EXECUTABLE@">Digestor</token>
     <import>macros.xml</import>
@@ -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
@@ -39,30 +38,37 @@
     <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="input file" help=" select fasta data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
+    <param argument="-in" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/>
+    <param argument="-out_type" type="select" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
       <option value="fasta">fasta</option>
       <option value="idXML">idxml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
-    <param argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/>
-    <param argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The type of digestion enzyme" 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>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
+    <param argument="-min_length" type="integer" value="6" label="Minimum length of peptide" help=""/>
+    <param argument="-max_length" type="integer" value="40" label="Maximum length of peptide" help=""/>
+    <param argument="-enzyme" type="select" label="The type of digestion enzyme" help="">
       <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</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="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="TrypChymo">TrypChymo</option>
+      <option value="Trypsin/P">Trypsin/P</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="Asp-N_ambic">Asp-N_ambic</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Chymotrypsin/P">Chymotrypsin/P</option>
@@ -72,26 +78,20 @@
       <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="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="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
     <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
-      <param name="ID" argument="-FASTA:ID" type="select" optional="true" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
+      <param name="ID" argument="-FASTA:ID" type="select" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
         <option value="parent" selected="true">parent</option>
         <option value="number">number</option>
         <option value="both">both</option>
         <expand macro="list_string_san" name="ID"/>
       </param>
-      <param name="description" argument="-FASTA:description" type="select" optional="true" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
+      <param name="description" argument="-FASTA:description" type="select" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
         <option value="remove" selected="true">remove</option>
         <option value="keep">keep</option>
         <expand macro="list_string_san" name="description"/>
@@ -99,7 +99,7 @@
     </section>
     <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>
@@ -117,16 +117,18 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="random.fa"/>
-    <output name="out" ftype="fasta" value="Digestor.fasta"/>
-    <param name="out_type" value="fasta"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="fasta" value="random.fa"/>
+      <output name="out" ftype="fasta" value="Digestor.fasta"/>
+      <param name="out_type" value="fasta"/>
+    </test>
+  </tests>
   <help><![CDATA[Digests a protein database in-silico.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Digestor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_Digestor.html]]></help>
   <expand macro="references"/>
 </tool>