Mercurial > repos > iuc > phyloseq_from_dada2
diff phyloseq_from_dada2.xml @ 0:46a99bd1f10e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
| author | iuc |
|---|---|
| date | Thu, 03 Mar 2022 13:28:04 +0000 |
| parents | |
| children | b85ba18a8f36 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_from_dada2.xml Thu Mar 03 13:28:04 2022 +0000 @@ -0,0 +1,35 @@ +<tool id="phyloseq_from_dada2" name="Create phyloseq object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>from dada2 sequence and taxonomy tables</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +Rscript '${__tool_directory__}/phyloseq_from_dada2.R' +--sequence_table '$sequence_table' +--taxonomy_table '$taxonomy_table' +--output '$output' + ]]></command> + <inputs> + <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/> + <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/> + </inputs> + <outputs> + <data name="output" format="phyloseq"/> + </outputs> + <tests> + <test> + <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/> + <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/> + <output name="output" value="output.phyloseq" ftype="phyloseq" compare="sim_size"/> + </test> + </tests> + <help> +**What it does** + +Accepts a sequence table produced by the dada2 removeBimeraDenovo tool and a taxonomy table produced by the +dada2 assignTaxonomyAndAddSpecies tool and uses them to create a phyloseq object which is output in a phyloseq dataset. + </help> + <expand macro="citations"/> +</tool> +