Mercurial > repos > iuc > phyloseq_from_dada2
comparison phyloseq_from_dada2.xml @ 2:87064cb77a52 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
author | iuc |
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date | Sat, 16 Mar 2024 07:55:48 +0000 |
parents | b85ba18a8f36 |
children |
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1:b85ba18a8f36 | 2:87064cb77a52 |
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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 |