Mercurial > repos > iuc > phyloseq_from_dada2
comparison 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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| -1:000000000000 | 0:46a99bd1f10e |
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| 1 <tool id="phyloseq_from_dada2" name="Create phyloseq object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description>from dada2 sequence and taxonomy tables</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 Rscript '${__tool_directory__}/phyloseq_from_dada2.R' | |
| 9 --sequence_table '$sequence_table' | |
| 10 --taxonomy_table '$taxonomy_table' | |
| 11 --output '$output' | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/> | |
| 15 <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="output" format="phyloseq"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/> | |
| 23 <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/> | |
| 24 <output name="output" value="output.phyloseq" ftype="phyloseq" compare="sim_size"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 **What it does** | |
| 29 | |
| 30 Accepts a sequence table produced by the dada2 removeBimeraDenovo tool and a taxonomy table produced by the | |
| 31 dada2 assignTaxonomyAndAddSpecies tool and uses them to create a phyloseq object which is output in a phyloseq dataset. | |
| 32 </help> | |
| 33 <expand macro="citations"/> | |
| 34 </tool> | |
| 35 |