Mercurial > repos > galaxyp > openms_novoradapter

diff NovorAdapter.xml @ 5:34dda034b019 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:20:30 +0000
parents 031adfb7fce0
children fa544e12732f
line wrap: on
line diff
--- a/NovorAdapter.xml	Mon Dec 14 16:52:37 2020 +0000
+++ b/NovorAdapter.xml	Thu Dec 01 19:20:30 2022 +0000
@@ -1,13 +1,11 @@
 <?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]-->
-<tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
-  <description>Template for Tool creation</description>
+<tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Performs de novo sequencing of peptides from MS/MS data with Novor.</description>
   <macros>
     <token name="@EXECUTABLE@">NovorAdapter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -49,31 +47,30 @@
     <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
-    <param name="enzyme" argument="-enzyme" display="radio" type="select" optional="false" label="Digestion enzyme - currently only Trypsin is supported" help="">
+    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
+    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme - currently only Trypsin is supported" help="">
       <option value="Trypsin" selected="true">Trypsin</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param name="fragmentation" argument="-fragmentation" display="radio" type="select" optional="false" label="Fragmentation method" help="">
+    <param argument="-fragmentation" type="select" optional="true" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="fragmentation"/>
     </param>
-    <param name="massAnalyzer" argument="-massAnalyzer" display="radio" type="select" optional="false" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
+    <param argument="-massAnalyzer" type="select" optional="true" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
       <option value="Trap" selected="true">Trap</option>
       <option value="TOF">TOF</option>
       <option value="FT">FT</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="massAnalyzer"/>
     </param>
-    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
-    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
-    <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
+    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
+    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
+    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help="">
-      <option value="">default (nothing chosen)</option>
+    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help="">
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Amidated (C-term)">Amidated (C-term)</option>
@@ -100,10 +97,9 @@
       <option value="Sodium (DE)">Sodium (DE)</option>
       <option value="Sulfo (STY)">Sulfo (STY)</option>
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param name="fixed_modifications" argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help="">
-      <option value="">default (nothing chosen)</option>
+    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help="">
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Amidated (C-term)">Amidated (C-term)</option>
@@ -130,19 +126,18 @@
       <option value="Sodium (DE)">Sodium (DE)</option>
       <option value="Sulfo (STY)">Sulfo (STY)</option>
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param name="forbiddenResidues" argument="-forbiddenResidues" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
-      <option value="">default (nothing chosen)</option>
+    <param argument="-forbiddenResidues" display="checkboxes" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
       <option value="I">I</option>
       <option value="U">U</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="forbiddenResidues"/>
     </param>
-    <param name="novorFile" argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/>
+    <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/>
     <expand macro="adv_opts_macro">
-      <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 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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -155,13 +150,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_NovorAdapter"/>
-    <expand macro="manutest_NovorAdapter"/>
+  <tests><!-- TOPP_NovorAdapter_1 -->
   </tests>
-  <help><![CDATA[Template for Tool creation
+  <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_NovorAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NovorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>