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comparison phyloseq_abundance_taxonomy.xml @ 0:b2fafdd3533d draft default tip

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:07:43 +0000
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1 <tool id="phyloseq_taxonomy" name="Phyloseq Abundance Taxonomy" version="1.22.3.3" hidden="false">
2 <description>Phyloseq Abundance Plot on Taxonomy level</description>
3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
6 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 <requirement type="package" version="9.18">ghostscript</requirement>
8 </requirements>
9 <version_command><![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
11 ]]></version_command>
12 <command detect_errors="exit_code"><![CDATA[
13 Rscript '${__tool_directory__}/phyloseq_abundance_taxonomy.r'
14 --biomfile='$biom_input'
15 --metafile='$metadata_input'
16 --xcolumn="${xaxis_column}"
17 --lcolumn="${legend_column}"
18 --taxonomy="${taxonomy_rank}"
19 --outdir="$htmlfile.files_path"
20 --htmlfile='$htmlfile'
21 ]]></command>
22
23 <inputs>
24 <param format="biom1" name="biom_input" type="data" label="BIOM file"/>
25 <param format="tabular" name="metadata_input" type="data" label="Metadata file"/>
26 <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/>
27 <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/>
28 <param name="taxonomy_rank" type="select" display="radio" label="Select a taxonomy rank">
29 <option value="Kingdom" selected="true">Kingdom</option>
30 <option value="Phylum">Phylum</option>
31 <option value="Class">Class</option>
32 <option value="Order">Order</option>
33 <option value="Family">Family</option>
34 <option value="Genus">Genus</option>
35 <option value="Species">Species</option>
36 </param>
37 </inputs>
38
39 <outputs>
40 <data format="html" name="htmlfile" label="${tool.name}.html"/>
41 </outputs>
42
43 <tests>
44 <test>
45 <param name="biom_input" value="test.biom" ftype="biom1" />
46 <param name="metadata_input" value="metadata.txt" />
47 <param name="xaxis_column" value="5" />
48 <param name="legend_column" value="4" />
49 <param name="taxonomy_rank" value="Phylum" />
50 <output name="htmlfile" ftype="html" file="biom_out.html" />
51 </test>
52 </tests>
53 <help>
54 **What it does**
55 Creates an abundance with taxonomy barplot using an R package called phyloseq_.
56
57 .. _phyloseq: https://joey711.github.io/phyloseq/plot_bar-examples.html
58
59 -----
60
61 **Input**
62
63
64 - **BIOM file** - this is a BIOM_ file format
65 - **Metadata file** - this is a metadata file of the experiment design
66 - **Column used for X-axis** - The horizontal x-axis display on the barplot.
67 - **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to.
68 - **Select a taxonomy rank** - This is a taxonomy selection.
69
70
71 .. _BIOM: http://biom-format.org/
72
73 -----
74
75 =========
76 Resources
77 =========
78
79 **Wrapper Authors**
80 QFAB Bioinformatics (support@qfab.org)
81
82 </help>
83 <citations>
84 <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
85 </citations>
86 </tool>