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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
author | iuc |
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date | Tue, 03 Dec 2024 17:45:38 +0000 |
parents | c0101c72b8af |
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<tool id="phyloseq_from_biom" name="Create phyloseq object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>from a BIOM file</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ Rscript '${__tool_directory__}/phyloseq_from_biom.R' --BIOMfilename '$BIOMfilename' #if $treefilename --treefilename '$treefilename' --parseFunction $parseFunction #end if #if $refseqfilename --refseqfilename '$refseqfilename' #end if --output '$output' ]]></command> <inputs> <param argument="BIOMfilename" type="data" format="biom1,biom2" label="BIOM file" help=""/> <param argument="treefilename" type="data" format="nex,newick" optional="true" label="Phylogeny" help=""/> <param name="parseFunction" type="select" label="Tree label parser" help=""> <option value="parse_taxonomy_default">Default</option> <option value="parse_taxonomy_greengenes">Greengenes</option> <option value="parse_taxonomy_qiime">Qiime</option> </param> <param argument="refseqfilename" type="data" format="fasta" optional="true" label="Sequences" help=""/> </inputs> <outputs> <data name="output" format="phyloseq"/> </outputs> <tests> <test> <param name="BIOMfilename" value="rich_dense_otu_table.biom" ftype="biom1"/> <output name="output"> <assert_contents> <has_size value="880" delta="100"/> </assert_contents> </output> <assert_stdout> <has_line line="phyloseq-class experiment-level object"/> <has_line line="otu_table() OTU Table: [ 5 taxa and 6 samples ]"/> <has_line line="sample_data() Sample Data: [ 6 samples by 4 sample variables ]"/> <has_line line="tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ]"/> <has_n_lines n="4"/> </assert_stdout> </test> <test> <param name="BIOMfilename" value="rich_dense_otu_table.biom2" ftype="biom2"/> <output name="output"> <assert_contents> <has_size value="880" delta="100"/> </assert_contents> </output> <assert_stdout> <has_line line="phyloseq-class experiment-level object"/> <has_line line="otu_table() OTU Table: [ 5 taxa and 6 samples ]"/> <has_line line="sample_data() Sample Data: [ 6 samples by 4 sample variables ]"/> <has_line line="tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ]"/> <has_n_lines n="4"/> </assert_stdout> </test> <test> <param name="BIOMfilename" value="rich_dense_otu_table.biom" ftype="biom1"/> <param name="treefilename" value="biom-tree.phy"/> <param name="parseFunction" value="parse_taxonomy_greengenes"/> <param name="refseqfilename" value="biom-refseq.fasta"/> <output name="output"> <assert_contents> <has_size value="1880" delta="200"/> </assert_contents> </output> <assert_stdout> <has_line line="phyloseq-class experiment-level object"/> <has_line line="otu_table() OTU Table: [ 5 taxa and 6 samples ]"/> <has_line line="sample_data() Sample Data: [ 6 samples by 4 sample variables ]"/> <has_line line="tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ]"/> <has_line line="phy_tree() Phylogenetic Tree: [ 5 tips and 4 internal nodes ]"/> <has_line line="refseq() DNAStringSet: [ 5 reference sequences ]"/> <has_n_lines n="6"/> </assert_stdout> </test> </tests> <help> **What it does** Read a BIOM file (and optionally sequences and a phylogeny) and store them in a phyloseq object. </help> <expand macro="citations"/> </tool>