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1 <tool id="phyloseq_ordinate" name="Phyloseq Ordination Plot" version="1.22.3.2" hidden="false">
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2 <description>ordination plotting</description>
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3 <requirements>
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4 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.0.11">r-doparallel</requirement>
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7 <requirement type="package" version="9.18">ghostscript</requirement>
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8 </requirements>
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9 <version_command><![CDATA[
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10 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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11 ]]></version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript '${__tool_directory__}/phyloseq_ordinate_plot.R'
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14 #if str($file_source.file_source_selector) == "set_biom":
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15 --biom='$file_source.input'
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16 --subset='$file_source.subsetColumn'
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17 #else:
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18 --otu_table='$OTU_TABLE'
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19 --tax_table='$TAX_TABLE'
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20 --meta_table='$META_TABLE'
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21 --category='$file_source.category'
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22 #end if
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23 #if str($plot_selection.plot_type) == "2":
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24 --plottype='$plot_selection.plot_type'
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25 --kingdom='null'
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26 #else:
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27 --plottype='$plot_selection.plot_type'
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28 --kingdom='$plot_selection.kingdom_field'
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29 #end if
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30 --method='$ord_method'
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31 --distance='$distance'
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32 --log='$log'
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33 --outdir="$htmlfile.files_path"
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34 --htmlfile='$htmlfile'
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35 ]]>
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36 </command>
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37
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38 <inputs>
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39 <conditional name="file_source">
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40 <param name="file_source_selector" type="select" label="Choose an input file type">
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41 <option value="set_biom" selected="True">BIOM File</option>
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42 <option value="set_table">TABULAR File</option>
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43 </param>
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44 <when value="set_biom">
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45 <param format="biom1" name="input" type="data" label="Input File"/>
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46 <param name="subsetColumn" type="select" label="Classify plot by">
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47 <options>
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48 <filter type="data_meta" ref="input" key="table_column_metadata_headers" />
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49 </options>
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50 </param>
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51 </when>
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52 <when value="set_table">
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53 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/>
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54 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/>
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55 <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/>
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56 <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Classify plot by"/>
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57 </when>
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58 </conditional>
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59 <param name="ord_method" type="select" display="radio" label="Select Ordination method">
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60 <option value="NMDS" selected="true">NMDS(Non-metric Multidimensional Scalling)</option>
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61 <option value="DCA">DCA (Detrended Correspondence Analysis)</option>
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62 <option value="CCA">CCA (Constrained Correspondence Analysis)</option>
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63 <option value="RDA">RDA (Redundancy Analysis)</option>
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64 <option value="DPCoA">DPCoA (Double Principle Coordinate Analysis)</option>
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65 <option value="MDS">MDS (Multidimensional Scaling)</option>
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66 <option value="PCoA">PCoA (Principal Coordinate Analysis)</option>
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67 </param>
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68 <param name="distance" type="select" display="radio" label="Select Distance method">
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69 <option value="bray" selected="true">bray (Bray-Curtis distance)</option>
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70 <option value="gower">gower (Gower's distance)</option>
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71 <option value="jsd">jds (Jensen-Shannon Divergence)</option>
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72 <option value="unifrac">unifrac (unweighted UniFrac distance)</option>
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73 <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option>
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74 </param>
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75 <!-- <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
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76 <option value="Kingdom">Kingdom</option>
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77 <option value="Phylum" selected="true">Phylum</option>
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78 <option value="Class">Class</option>
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79 <option value="Order">Order</option>
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80 <option value="Family">Family</option>
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81 <option value="Genus">Genus</option>
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82 <option value="Species">Species</option>
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83 </param>
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84 -->
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85 <conditional name="plot_selection">
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86 <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)">
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87 <option value="1">OTU</option>
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88 <option value="2" selected="true">SAMPLE</option>
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89 <option value="3">BIPLOT</option>
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90 <option value="4">SPLIT PLOT</option>
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91 </param>
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92 <when value="1">
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93 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
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94 <option value="Kingdom">Kingdom</option>
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95 <option value="Phylum" selected="true">Phylum</option>
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96 <option value="Class">Class</option>
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97 <option value="Order">Order</option>
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98 <option value="Family">Family</option>
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99 <option value="Genus">Genus</option>
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100 <option value="Species">Species</option>
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101 </param>
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102 </when>
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103 <when value="2">
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104 </when>
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105 <when value="3">
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106 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
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107 <option value="Kingdom">Kingdom</option>
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108 <option value="Phylum" selected="true">Phylum</option>
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109 <option value="Class">Class</option>
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110 <option value="Order">Order</option>
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111 <option value="Family">Family</option>
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112 <option value="Genus">Genus</option>
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113 <option value="Species">Species</option>
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114 </param>
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115 </when>
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116 <when value="4">
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117 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
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118 <option value="Kingdom">Kingdom</option>
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119 <option value="Phylum" selected="true">Phylum</option>
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120 <option value="Class">Class</option>
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121 <option value="Order">Order</option>
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122 <option value="Family">Family</option>
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123 <option value="Genus">Genus</option>
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124 <option value="Species">Species</option>
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125 </param>
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126 </when>
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127 </conditional>
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128 </inputs>
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129 <outputs>
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130 <data format="txt" name="log" label="${tool.name} - stress value - distance matrix - sample column sum"/>
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131 <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/>
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132 </outputs>
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133
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134 <tests>
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135 <test> <!-- Test #1: Test BIOM format input -->
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136 <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +biom=test-data/GP.biom +subset=6 +method=NMDS
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137 +distance=bray +kingdom=Phylum +cutoff=5 +keep=5 +outdir=outputdir +htmlfile=biom_out.html -->
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138 <conditional name="file_source">
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139 <param name="file_source_selector" value="set_biom"/>
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140 <param name="input" value="GP.biom" ftype="biom1"/>
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141 <param name="subsetColumn" value="Primer" />
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142 </conditional>
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143 <output name="htmlfile" ftype="html" file="biom_out.html" />
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144 </test>
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145 <test> <!-- Test #2: Test TABULAR format inputs -->
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146 <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +otu_table=test-data/GP_OTU_TABLE.txt
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147 +tax_table=test-data/GP_TAX_TABLE.txt +meta_table=test-data/GP_SAMPLE_TABLE.txt
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148 +method="bray" +kingdom=Phylum +cutoff=5 + keep=5 +category=6 +outdir=outputdir +htmlfile=test.html -->
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149 <conditional name="file_source">
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150 <param name="file_source_selector" value="set_table" />
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151 <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" />
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152 <param name="TAX_TABLE" value="GP_TAX_TABLE.txt" />
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153 <param name="META_TABLE" value="GP_SAMPLE_TABLE.txt" />
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154 <param name="category" value="6" />
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155 </conditional>
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156 <output name="htmlfile" ftype="html" file="test.html" />
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157 </test>
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158 </tests>
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159
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160 <help>
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161 **What it does**
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162 Creates various ordination plot using an R_package_called_phyloseq_,specifically according to the methods outlined in the Phyloseq_Ordination_Plot_Tutorial_.
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163
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164 .. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html
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165 .. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html
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166
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167 -----
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168
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169 **Input**
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170
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171 - **Choose an input file type** - either 1 BIOM File or 3 TABULAR files (OTU, taxonomy and Metadata tables)
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172 - **Classify plot by** - points on the plot will be colour coded according to their value of the selected feature
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173 - **Select Ordination method** - several methods are supported
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174 - **Select Distance method** - several methods are supported
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175 - **Select a taxonomic rank for the analysis** - select a taxonomy for ordination plot
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176
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177 -----
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178
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179 =========
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180 Resources
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181 =========
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182
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183 **Wrapper Authors**
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184
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185 QFAB Bioinformatics (support@qfab.org)
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186 Melbourne Bioinformatics
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187 </help>
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188 <citations>
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189 <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
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190 </citations>
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191 </tool>
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