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comparison phyloseq_from_dada2.xml @ 2:87064cb77a52 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
author iuc
date Sat, 16 Mar 2024 07:55:48 +0000
parents b85ba18a8f36
children
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1:b85ba18a8f36 2:87064cb77a52
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '${__tool_directory__}/phyloseq_from_dada2.R' 9 Rscript '${__tool_directory__}/phyloseq_from_dada2.R'
10 --sequence_table '$sequence_table' 10 --sequence_table '$sequence_table'
11 --taxonomy_table '$taxonomy_table' 11 --taxonomy_table '$taxonomy_table'
12 #if $sample_table
13 --sample_table '$sample_table'
14 #end if
12 --output '$output' 15 --output '$output'
13 ]]></command> 16 ]]></command>
14 <inputs> 17 <inputs>
15 <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/> 18 <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/>
16 <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/> 19 <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/>
20 <param name="sample_table" type="data" format="tabular" optional="true" label="Sample table" help="Rows are sample names, Columns are properties"/>
17 </inputs> 21 </inputs>
18 <outputs> 22 <outputs>
19 <data name="output" format="phyloseq"/> 23 <data name="output" format="phyloseq"/>
20 </outputs> 24 </outputs>
21 <tests> 25 <tests>
22 <test> 26 <test>
23 <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/> 27 <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
24 <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/> 28 <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
25 <output name="output" value="output.phyloseq" ftype="phyloseq" compare="sim_size"/> 29 <output name="output" ftype="phyloseq">
30 <assert_contents>
31 <has_size value="4600" delta="400"/>
32 </assert_contents>
33 </output>
34 <assert_stdout>
35 <has_text text="phyloseq-class experiment-level object"/>
36 <has_text text="otu_table() OTU Table: [ 64 taxa and 2 samples ]"/>
37 <has_text text="tax_table() Taxonomy Table: [ 64 taxa by 6 taxonomic ranks ]"/>
38 <has_text text="refseq() DNAStringSet: [ 64 reference sequences ]"/>
39 <has_n_lines n="4"/>
40 </assert_stdout>
41 </test>
42 <test>
43 <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
44 <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
45 <param name="sample_table" value="sample_data.tabular" ftype="tabular"/>
46 <output name="output" ftype="phyloseq">
47 <assert_contents>
48 <has_size value="4600" delta="400"/>
49 </assert_contents>
50 </output>
51 <assert_stdout>
52 <has_line line="phyloseq-class experiment-level object"/>
53 <has_line line="otu_table() OTU Table: [ 64 taxa and 2 samples ]"/>
54 <has_line line="sample_data() Sample Data: [ 2 samples by 2 sample variables ]"/>
55 <has_line line="tax_table() Taxonomy Table: [ 64 taxa by 6 taxonomic ranks ]"/>
56 <has_line line="refseq() DNAStringSet: [ 64 reference sequences ]"/>
57 <has_n_lines n="5"/>
58 </assert_stdout>
26 </test> 59 </test>
27 </tests> 60 </tests>
28 <help> 61 <help>
29 **What it does** 62 **What it does**
30 63