Repository 'ampvis2_load'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load

Changeset 5:91efbd7b52dc (2024-08-16)
Previous changeset 4:3481feabc54e (2024-03-16) Next changeset 6:576dd33588bf (2024-08-26)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
modified:
macros.xml
added:
test-data/AalborgWWTPs-metadata_NA.list
b
diff -r 3481feabc54e -r 91efbd7b52dc macros.xml
--- a/macros.xml Sat Mar 16 11:34:24 2024 +0000
+++ b/macros.xml Fri Aug 16 08:57:56 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
b
diff -r 3481feabc54e -r 91efbd7b52dc 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 08:57:56 2024 +0000
b
@@ -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