Mercurial > repos > iuc > ampvis2_export_otu

comparison export_otu.xml @ 1:f92f6cb141fd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 commit e0ad9ce8f508215ec6af69be2682a0faf38415da
author iuc
date Mon, 10 Nov 2025 12:50:02 +0000
parents adab1cdb8811
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0:adab1cdb8811 1:f92f6cb141fd
1 <tool id="ampvis2_export_otu" name="ampvis2 export otu" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> 1 <tool id="ampvis2_export_otu" name="ampvis2 export otu" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="header"/> 6 <expand macro="header"/>
38 ## add index col manually: https://stackoverflow.com/questions/2478352/write-table-writes-unwanted-leading-empty-column-to-header-when-has-rownames 38 ## add index col manually: https://stackoverflow.com/questions/2478352/write-table-writes-unwanted-leading-empty-column-to-header-when-has-rownames
39 write.table(otu_table, "$otu_short", sep = "\t", row.names=FALSE, quote = FALSE) 39 write.table(otu_table, "$otu_short", sep = "\t", row.names=FALSE, quote = FALSE)
40 40
41 ## get metadata 41 ## get metadata
42 meta_data = data\$metadata 42 meta_data = data\$metadata
43 write.table(meta_data, "$meta", sep = "\t", col.names=NA, quote = FALSE) 43 write.table(meta_data, "$meta", sep = "\t", row.names = FALSE, quote = FALSE)
44 44
45 ## needs to be numeric 45 ## needs to be numeric
46 otu_table <- apply(otu_table, 2, as.numeric) 46 otu_table <- apply(otu_table, 2, as.numeric)
47 47
48 ## needs to be character so that reupload as ampvis object works 48 ## needs to be character so that reupload as ampvis object works