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comparison phyloseq_ordinate_plot.xml @ 0:ae9cd53b7760 draft

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Initial upload
author simon-gladman
date Wed, 05 Sep 2018 02:07:22 -0400
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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>