Mercurial > repos > iuc > phyloseq_from_dada2

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d6888da7aba38b97f6cb827355f2de436565684a
author iuc
date Tue, 04 Feb 2025 14:39:44 +0000
parents 87064cb77a52
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1 <tool id="phyloseq_from_dada2" name="Create phyloseq object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from dada2 sequence and taxonomy tables</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '${__tool_directory__}/phyloseq_from_dada2.R'
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10 --sequence_table '$sequence_table'
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11 --taxonomy_table '$taxonomy_table'
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12 #if $sample_table
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13 --sample_table '$sample_table'
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14 #end if
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15 --output '$output'
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16 ]]></command>
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17 <inputs>
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18 <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/>
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19 <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/>
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20 <param name="sample_table" type="data" format="tabular" optional="true" label="Sample table" help="Rows are sample names, Columns are properties"/>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="phyloseq"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
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28 <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
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29 <output name="output" ftype="phyloseq">
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30 <assert_contents>
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31 <has_size value="4600" delta="400"/>
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32 </assert_contents>
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33 </output>
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34 <assert_stdout>
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35 <has_text text="phyloseq-class experiment-level object"/>
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36 <has_text text="otu_table() OTU Table: [ 64 taxa and 2 samples ]"/>
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37 <has_text text="tax_table() Taxonomy Table: [ 64 taxa by 6 taxonomic ranks ]"/>
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38 <has_text text="refseq() DNAStringSet: [ 64 reference sequences ]"/>
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39 <has_n_lines n="4"/>
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40 </assert_stdout>
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41 </test>
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42 <test>
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43 <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
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44 <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
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45 <param name="sample_table" value="sample_data.tabular" ftype="tabular"/>
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46 <output name="output" ftype="phyloseq">
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47 <assert_contents>
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48 <has_size value="4600" delta="400"/>
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49 </assert_contents>
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50 </output>
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51 <assert_stdout>
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52 <has_line line="phyloseq-class experiment-level object"/>
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53 <has_line line="otu_table() OTU Table: [ 64 taxa and 2 samples ]"/>
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54 <has_line line="sample_data() Sample Data: [ 2 samples by 2 sample variables ]"/>
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55 <has_line line="tax_table() Taxonomy Table: [ 64 taxa by 6 taxonomic ranks ]"/>
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56 <has_line line="refseq() DNAStringSet: [ 64 reference sequences ]"/>
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57 <has_n_lines n="5"/>
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58 </assert_stdout>
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59 </test>
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60 </tests>
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61 <help>
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62 **What it does**
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63
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64 Accepts a sequence table produced by the dada2 removeBimeraDenovo tool and a taxonomy table produced by the
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65 dada2 assignTaxonomyAndAddSpecies tool and uses them to create a phyloseq object which is output in a phyloseq dataset.
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66 </help>
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67 <expand macro="citations"/>
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68 </tool>
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69