| Previous changeset 4:c8bfb923d7d4 (2024-03-16) Next changeset 6:f9fa155c191f (2024-08-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf |
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modified:
macros.xml subset_samples.xml |
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added:
test-data/AalborgWWTPs-metadata_NA.list |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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	Aalborg East	FALSE	character"/> + <not_has_text text="SampleID	NA	TRUE	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"/> |
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| 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 |
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| @@ -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 |