# HG changeset patch
# User iuc
# Date 1723798902 0
# Node ID 317728cb0f8af01851b5e1caafbf0a1b1139c875
# Parent  c8bfb923d7d40a58fc2f82ab02e3977c05c8ce00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf

diff -r c8bfb923d7d4 -r 317728cb0f8a macros.xml
--- a/macros.xml	Sat Mar 16 11:31:10 2024 +0000
+++ b/macros.xml	Fri Aug 16 09:01:42 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.8.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="header">
         <xrefs>
@@ -44,6 +44,7 @@
 
     <token name="@SAVE_METADATA_LIST@"><![CDATA[
                 classes <- sapply(data\$metadata, class)
+                data\$metadata[is.na(data\$metadata)] <- "NA" ##the comparison below fails if NA values are present, see https://stackoverflow.com/questions/7355187/error-in-if-while-condition-missing-value-where-true-false-needed
                 for(name in names(data\$metadata)){
                     ## check if it is the column containing the sample names
                     ## the additional column in the ist file can the be used
diff -r c8bfb923d7d4 -r 317728cb0f8a subset_samples.xml
--- a/subset_samples.xml	Sat Mar 16 11:31:10 2024 +0000
+++ b/subset_samples.xml	Fri Aug 16 09:01:42 2024 +0000
@@ -62,6 +62,22 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- test NA values in metadata -->
+        <test expect_num_outputs="2">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata_NA.list"/>
+            <param name="var" value="Plant"/>
+            <param name="vals" value="Aalborg East"/>
+            <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
+            <output name="metadata_list_out" ftype="tabular">
+                <assert_contents>
+                    <has_line line="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
+                    <not_has_text text="SampleID&#9;NA&#9;TRUE&#9;character"/>
+                    <has_n_lines n="85"/>
+                    <has_n_columns n="4"/>
+                </assert_contents>
+            </output>
+        </test>
         <!-- invert -->
         <test expect_num_outputs="2">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
diff -r c8bfb923d7d4 -r 317728cb0f8a test-data/AalborgWWTPs-metadata_NA.list
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AalborgWWTPs-metadata_NA.list	Fri Aug 16 09:01:42 2024 +0000
@@ -0,0 +1,125 @@
+SampleID	16SAMP-747	TRUE	character
+SampleID	16S-AMP-1168	TRUE	character
+SampleID	16SAMP-4603	TRUE	character
+SampleID	16S-AMP-1149	TRUE	character
+SampleID	16SAMP-537	TRUE	character
+SampleID	16S-AMP-1114	TRUE	character
+SampleID	16SAMP-3893	TRUE	character
+SampleID	16SAMP-703	TRUE	character
+SampleID	16SAMP-638	TRUE	character
+SampleID	16SAMP-2611	TRUE	character
+SampleID	16S-AMP-1100	TRUE	character
+SampleID	16SAMP-608	TRUE	character
+SampleID	16SAMP-636	TRUE	character
+SampleID	16SAMP-13288	TRUE	character
+SampleID	16SAMP-719	TRUE	character
+SampleID	16S-AMP-1098	TRUE	character
+SampleID	16SAMP-536	TRUE	character
+SampleID	16S-AMP-1169	TRUE	character
+SampleID	16SAMP-635	TRUE	character
+SampleID	16SAMP-637	TRUE	character
+SampleID	16SAMP-717	TRUE	character
+SampleID	16S-AMP-1148	TRUE	character
+SampleID	16SAMP-735	TRUE	character
+SampleID	16SAMP-729	TRUE	character
+SampleID	16SAMP-738	TRUE	character
+SampleID	16SAMP-2613	TRUE	character
+SampleID	16SAMP-10925	TRUE	character
+SampleID	16SAMP-3913	TRUE	character
+SampleID	16SAMP-716	TRUE	character
+SampleID	16SAMP-726	TRUE	character
+SampleID	16SAMP-728	TRUE	character
+SampleID	16SAMP-625	TRUE	character
+SampleID	16SAMP-736	TRUE	character
+SampleID	16SAMP-13281	TRUE	character
+SampleID	16SAMP-626	TRUE	character
+SampleID	16SAMP-704	TRUE	character
+SampleID	16SAMP-2612	TRUE	character
+SampleID	16SAMP-746	TRUE	character
+SampleID	16SAMP-522	TRUE	character
+SampleID	16SAMP-516	TRUE	character
+SampleID	16S-AMP-1170	TRUE	character
+SampleID	16S-AMP-1099	TRUE	character
+SampleID	16SAMP-10932	TRUE	character
+SampleID	16SAMP-740	TRUE	character
+SampleID	16SAMP-739	TRUE	character
+SampleID	16SAMP-4597	TRUE	character
+SampleID	16SAMP-535	TRUE	character
+SampleID	16SAMP-3941	TRUE	character
+SampleID	16SAMP-3953	TRUE	character
+SampleID	16SAMP-720	TRUE	character
+SampleID	16SAMP-705	TRUE	character
+SampleID	16SAMP-10907	TRUE	character
+SampleID	16SAMP-538	TRUE	character
+SampleID	16SAMP-10911	TRUE	character
+SampleID	16SAMP-737	TRUE	character
+SampleID	16SAMP-4591	TRUE	character
+SampleID	16SAMP-745	TRUE	character
+SampleID	16SAMP-706	TRUE	character
+SampleID	16SAMP-3946	TRUE	character
+SampleID	16S-AMP-1101	TRUE	character
+SampleID	16SAMP-10896	TRUE	character
+SampleID	16SAMP-10891	TRUE	character
+SampleID	16SAMP-748	TRUE	character
+SampleID	16SAMP-725	TRUE	character
+SampleID	16SAMP-730	TRUE	character
+SampleID	16S-AMP-1107	TRUE	character
+SampleID	NA	TRUE	character
+Plant	Aalborg East	FALSE	character
+Plant	Aalborg West	FALSE	character
+Date	14644	FALSE	Date
+Date	15831	FALSE	Date
+Date	16301	FALSE	Date
+Date	16006	FALSE	Date
+Date	14840	FALSE	Date
+Date	15740	FALSE	Date
+Date	16107	FALSE	Date
+Date	13183	FALSE	Date
+Date	15641	FALSE	Date
+Date	15009	FALSE	Date
+Date	15571	FALSE	Date
+Date	15275	FALSE	Date
+Date	15466	FALSE	Date
+Date	16475	FALSE	Date
+Date	13744	FALSE	Date
+Date	15374	FALSE	Date
+Date	14735	FALSE	Date
+Date	15936	FALSE	Date
+Date	13548	FALSE	Date
+Date	14005	FALSE	Date
+Date	14110	FALSE	Date
+Date	14279	FALSE	Date
+Date	15205	FALSE	Date
+Date	16735	FALSE	Date
+Date	16254	FALSE	Date
+Date	16476	FALSE	Date
+Date	13274	FALSE	Date
+Date	14370	FALSE	Date
+Date	14910	FALSE	Date
+Date	14545	FALSE	Date
+Date	16195	FALSE	Date
+Date	16300	FALSE	Date
+Date	16386	FALSE	Date
+Date	13814	FALSE	Date
+Date	13379	FALSE	Date
+Date	16671	FALSE	Date
+Date	14180	FALSE	Date
+Date	16105	FALSE	Date
+Date	13449	FALSE	Date
+Date	16387	FALSE	Date
+Date	16559	FALSE	Date
+Date	NA	FALSE	Date
+Year	2010	FALSE	integer
+Year	2013	FALSE	integer
+Year	2014	FALSE	integer
+Year	2006	FALSE	integer
+Year	2012	FALSE	integer
+Year	2011	FALSE	integer
+Year	2015	FALSE	integer
+Year	2007	FALSE	integer
+Year	2008	FALSE	integer
+Year	2009	FALSE	integer
+Period	Winter	FALSE	character
+Period	Spring	FALSE	character
+Period	Summer	FALSE	character
+Period	Fall	FALSE	character