Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation

diff annotationRmn2D_xml.xml @ 4:cf11fa0c47c8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
author workflow4metabolomics
date Thu, 23 Jan 2025 15:28:44 +0000
parents 546c7ccd2ed4
children
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--- a/annotationRmn2D_xml.xml	Fri Feb 04 09:01:11 2022 +0000
+++ b/annotationRmn2D_xml.xml	Thu Jan 23 15:28:44 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0" profile="20.09">
+<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0+galaxy2" profile="20.09">
 
     <description> Annotation of complex mixture bidimensional NMR spectra </description>
 
@@ -11,14 +11,25 @@
         <requirement type="package" version="1.0.2">r-tidyr</requirement>
         <requirement type="package" version="3.3">r-curl</requirement>
         <requirement type="package" version="1.6">r-jsonlite</requirement>
-        <requirement type="package">r-stringi</requirement>
+        <requirement type="package" version="1">r-stringi</requirement>
     </requirements>
-
+    <required_files>
+        <include path="annotationRmn2DWrapper.R" />
+        <include path="annotationRmn2D.R" />
+        <include path="annotationRmn2DGlobale.R" />
+        <include path="viridis.R" />
+        <include path="BdDReference_COSY.RData" />
+        <include path="BdDReference_HMBC.RData" />
+        <include path="BdDReference_HSQC.RData" />
+        <include path="BdDReference_JRES.RData" />
+        <include path="BdDReference_NOESY.RData" />
+        <include path="BdDReference_TOCSY.RData" />
+    </required_files>
     <stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command detect_errors="aggressive"><![CDATA[
         ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
         Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
 
@@ -86,7 +97,7 @@
         ppmCommunTOCSY '$ppmCommunTOCSY'
         annotationCombination '$annotationCombination'
         AnnotationGraph '$AnnotationGraph'
-    </command>
+    ]]></command>
 
     <inputs>
         <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
@@ -230,14 +241,16 @@
         <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
     </outputs>
     <tests>
-        <test expect_num_outputs="13">
+        <test expect_num_outputs="13" expect_test_failure="true">
             <param name="zip_xlsfile" value="Template_melange.xlsx" ftype="xlsx"/>
             <param name="cosy_2dsequences" value="yes"/>
             <param name="jres_2dsequences" value="yes"/>
             <param name="hmbc_2dsequences" value="yes"/>
             <param name="hsqc_2dsequences" value="yes"/>
             <param name="tocsy_2dsequences" value="yes"/>
-            <param name="inHouse_DB_choices.choice" value="no"/>
+            <section name="inHouse_DB_choices">
+            <param name="choice" value="no"/>
+            </section>
             <param name="tolppm1" value="0.01"/>
             <param name="tolppm2" value="0.5"/>
             <param name="tolppmJRES" value="0.002"/>