Mercurial > repos > iuc > phyloseq_from_biom
diff phyloseq_from_biom.xml @ 0:c0101c72b8af draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
| author | iuc |
|---|---|
| date | Sat, 16 Mar 2024 07:56:17 +0000 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_from_biom.xml Sat Mar 16 07:56:17 2024 +0000 @@ -0,0 +1,92 @@ +<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> +