|
0
|
1 <tool id="phyloseq_ordinate" name="Phyloseq Ordination Plot" version="1.22.3.2" hidden="false">
|
|
|
2 <description>ordination plotting</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
|
|
|
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
|
|
|
6 <requirement type="package" version="1.0.11">r-doparallel</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_ordinate_plot.R'
|
|
|
14 #if str($file_source.file_source_selector) == "set_biom":
|
|
|
15 --biom='$file_source.input'
|
|
|
16 --subset='$file_source.subsetColumn'
|
|
|
17 #else:
|
|
|
18 --otu_table='$OTU_TABLE'
|
|
|
19 --tax_table='$TAX_TABLE'
|
|
|
20 --meta_table='$META_TABLE'
|
|
|
21 --category='$file_source.category'
|
|
|
22 #end if
|
|
|
23 --method='$ord_method'
|
|
|
24 --distance='$distance'
|
|
|
25 --kingdom='$kingdom_field'
|
|
|
26 --plottype='$plot_type'
|
|
|
27 --outdir="$htmlfile.files_path"
|
|
|
28 --htmlfile='$htmlfile'
|
|
|
29 ]]>
|
|
|
30 </command>
|
|
|
31
|
|
|
32 <inputs>
|
|
|
33 <conditional name="file_source">
|
|
|
34 <param name="file_source_selector" type="select" label="Choose an input file type">
|
|
|
35 <option value="set_biom" selected="True">BIOM File</option>
|
|
|
36 <option value="set_table">TABULAR File</option>
|
|
|
37 </param>
|
|
|
38 <when value="set_biom">
|
|
|
39 <param format="biom1" name="input" type="data" label="Input File"/>
|
|
|
40 <param name="subsetColumn" type="select" label="Select variable for ordination">
|
|
|
41 <options>
|
|
|
42 <filter type="data_meta" ref="input" key="table_column_metadata_headers" />
|
|
|
43 </options>
|
|
|
44 </param>
|
|
|
45 </when>
|
|
|
46 <when value="set_table">
|
|
|
47 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/>
|
|
|
48 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/>
|
|
|
49 <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/>
|
|
|
50 <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Select variable for ordination"/>
|
|
|
51 </when>
|
|
|
52 </conditional>
|
|
|
53 <param name="ord_method" type="select" display="radio" label="Select Ordination method">
|
|
|
54 <option value="NMDS" selected="true">NMDS(Non-metric Multidimensional Scalling)</option>
|
|
|
55 <option value="DCA">DCA (Detrended Correspondence Analysis)</option>
|
|
|
56 <option value="CCA">CCA (Constrained Correspondence Analysis)</option>
|
|
|
57 <option value="RDA">RDA (Redundancy Analysis)</option>
|
|
|
58 <option value="DPCoA">DPCoA (Double Principle Coordinate Analysis)</option>
|
|
|
59 <option value="MDS">MDS (Multidimensional Scaling)</option>
|
|
|
60 <option value="PCoA">PCoA (Principal Coordinate Analysis)</option>
|
|
|
61 </param>
|
|
|
62 <param name="distance" type="select" display="radio" label="Select Distance method">
|
|
|
63 <option value="bray" selected="true">bray (Bray-Curtis distance)</option>
|
|
|
64 <option value="gower">gower (Gower's distance)</option>
|
|
|
65 <option value="jsd">jds (Jensen-Shannon Divergence)</option>
|
|
|
66 <option value="unifrac">unifrac (unweighted UniFrac distance)</option>
|
|
|
67 <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option>
|
|
|
68 </param>
|
|
|
69 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
|
|
|
70 <option value="Kingdom">Kingdom</option>
|
|
|
71 <option value="Phylum" selected="true">Phylum</option>
|
|
|
72 <option value="Class">Class</option>
|
|
|
73 <option value="Order">Order</option>
|
|
|
74 <option value="Family">Family</option>
|
|
|
75 <option value="Genus">Genus</option>
|
|
|
76 <option value="Species">Species</option>
|
|
|
77 </param>
|
|
|
78 <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)">
|
|
|
79 <option value="1">OTU</option>
|
|
|
80 <option value="2" selected="true">SAMPLE</option>
|
|
|
81 <option value="3">BIPLOT</option>
|
|
|
82 <option value="4">SPLIT PLOT</option>
|
|
|
83 </param>
|
|
|
84 </inputs>
|
|
|
85 <outputs>
|
|
|
86 <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/>
|
|
|
87 </outputs>
|
|
|
88
|
|
|
89 <tests>
|
|
|
90 <test> <!-- Test #1: Test BIOM format input -->
|
|
|
91 <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +biom=test-data/GP.biom +subset=6 +method=NMDS
|
|
|
92 +distance=bray +kingdom=Phylum +cutoff=5 +keep=5 +outdir=outputdir +htmlfile=biom_out.html -->
|
|
|
93 <conditional name="file_source">
|
|
|
94 <param name="file_source_selector" value="set_biom"/>
|
|
|
95 <param name="input" value="GP.biom" ftype="biom1"/>
|
|
|
96 <param name="subsetColumn" value="Primer" />
|
|
|
97 </conditional>
|
|
|
98 <output name="htmlfile" ftype="html" file="biom_out.html" />
|
|
|
99 </test>
|
|
|
100 <test> <!-- Test #2: Test TABULAR format inputs -->
|
|
|
101 <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +otu_table=test-data/GP_OTU_TABLE.txt
|
|
|
102 +tax_table=test-data/GP_TAX_TABLE.txt +meta_table=test-data/GP_SAMPLE_TABLE.txt
|
|
|
103 +method="bray" +kingdom=Phylum +cutoff=5 + keep=5 +category=6 +outdir=outputdir +htmlfile=test.html -->
|
|
|
104 <conditional name="file_source">
|
|
|
105 <param name="file_source_selector" value="set_table" />
|
|
|
106 <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" />
|
|
|
107 <param name="TAX_TABLE" value="GP_TAX_TABLE.txt" />
|
|
|
108 <param name="META_TABLE" value="GP_SAMPLE_TABLE.txt" />
|
|
|
109 <param name="category" value="6" />
|
|
|
110 </conditional>
|
|
|
111 <output name="htmlfile" ftype="html" file="test.html" />
|
|
|
112 </test>
|
|
|
113 </tests>
|
|
|
114
|
|
|
115 <help>
|
|
|
116 **What it does**
|
|
|
117 Creates NMDS plot using R package called phyloseq_.
|
|
|
118
|
|
|
119 .. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html
|
|
|
120
|
|
|
121 -----
|
|
|
122
|
|
|
123 **Input**
|
|
|
124
|
|
|
125 - **Choose an input file type** - BIOM File or TABULAR file
|
|
|
126 - **Select variable for ordination** - This column is used to extract unique value from the column of interest for ordination plot
|
|
|
127 - **OTU TABLE** - this is a OTU matrix
|
|
|
128 - **Taxonomy TABLE** - this is a TAX matrix
|
|
|
129 - **Metadata TABLE** - this is a metadata file of the experiment design
|
|
|
130 - **Select Ordination method** - select ordination method
|
|
|
131 - **Select Distance method** - select distance method for ordination plot
|
|
|
132 - **Select a taxonomic rank for the analysis** - select a taxonomy for ordination plot
|
|
|
133
|
|
|
134 -----
|
|
|
135
|
|
|
136 =========
|
|
|
137 Resources
|
|
|
138 =========
|
|
|
139
|
|
|
140 **Wrapper Authors**
|
|
|
141
|
|
|
142 QFAB Bioinformatics (support@qfab.org)
|
|
|
143 Melbourne Bioinformatics
|
|
|
144 </help>
|
|
|
145 <citations>
|
|
|
146 <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
|
|
|
147 </citations>
|
|
|
148 </tool>
|
