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comparison phyloseq_ordinate_plot.xml @ 1:52f009b255a1 draft default tip

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Updated tool
author simon-gladman
date Thu, 22 Nov 2018 07:07:27 -0500
parents ae9cd53b7760
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0:ae9cd53b7760 1:52f009b255a1
18 --otu_table='$OTU_TABLE' 18 --otu_table='$OTU_TABLE'
19 --tax_table='$TAX_TABLE' 19 --tax_table='$TAX_TABLE'
20 --meta_table='$META_TABLE' 20 --meta_table='$META_TABLE'
21 --category='$file_source.category' 21 --category='$file_source.category'
22 #end if 22 #end if
23 #if str($plot_selection.plot_type) == "2":
24 --plottype='$plot_selection.plot_type'
25 --kingdom='null'
26 #else:
27 --plottype='$plot_selection.plot_type'
28 --kingdom='$plot_selection.kingdom_field'
29 #end if
23 --method='$ord_method' 30 --method='$ord_method'
24 --distance='$distance' 31 --distance='$distance'
25 --kingdom='$kingdom_field' 32 --log='$log'
26 --plottype='$plot_type'
27 --outdir="$htmlfile.files_path" 33 --outdir="$htmlfile.files_path"
28 --htmlfile='$htmlfile' 34 --htmlfile='$htmlfile'
29 ]]> 35 ]]>
30 </command> 36 </command>
31 37
35 <option value="set_biom" selected="True">BIOM File</option> 41 <option value="set_biom" selected="True">BIOM File</option>
36 <option value="set_table">TABULAR File</option> 42 <option value="set_table">TABULAR File</option>
37 </param> 43 </param>
38 <when value="set_biom"> 44 <when value="set_biom">
39 <param format="biom1" name="input" type="data" label="Input File"/> 45 <param format="biom1" name="input" type="data" label="Input File"/>
40 <param name="subsetColumn" type="select" label="Select variable for ordination"> 46 <param name="subsetColumn" type="select" label="Classify plot by">
41 <options> 47 <options>
42 <filter type="data_meta" ref="input" key="table_column_metadata_headers" /> 48 <filter type="data_meta" ref="input" key="table_column_metadata_headers" />
43 </options> 49 </options>
44 </param> 50 </param>
45 </when> 51 </when>
46 <when value="set_table"> 52 <when value="set_table">
47 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/> 53 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/>
48 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/> 54 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/>
49 <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/> 55 <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"/> 56 <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Classify plot by"/>
51 </when> 57 </when>
52 </conditional> 58 </conditional>
53 <param name="ord_method" type="select" display="radio" label="Select Ordination method"> 59 <param name="ord_method" type="select" display="radio" label="Select Ordination method">
54 <option value="NMDS" selected="true">NMDS(Non-metric Multidimensional Scalling)</option> 60 <option value="NMDS" selected="true">NMDS(Non-metric Multidimensional Scalling)</option>
55 <option value="DCA">DCA (Detrended Correspondence Analysis)</option> 61 <option value="DCA">DCA (Detrended Correspondence Analysis)</option>
64 <option value="gower">gower (Gower's distance)</option> 70 <option value="gower">gower (Gower's distance)</option>
65 <option value="jsd">jds (Jensen-Shannon Divergence)</option> 71 <option value="jsd">jds (Jensen-Shannon Divergence)</option>
66 <option value="unifrac">unifrac (unweighted UniFrac distance)</option> 72 <option value="unifrac">unifrac (unweighted UniFrac distance)</option>
67 <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option> 73 <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option>
68 </param> 74 </param>
69 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> 75 <!-- <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
70 <option value="Kingdom">Kingdom</option> 76 <option value="Kingdom">Kingdom</option>
71 <option value="Phylum" selected="true">Phylum</option> 77 <option value="Phylum" selected="true">Phylum</option>
72 <option value="Class">Class</option> 78 <option value="Class">Class</option>
73 <option value="Order">Order</option> 79 <option value="Order">Order</option>
74 <option value="Family">Family</option> 80 <option value="Family">Family</option>
75 <option value="Genus">Genus</option> 81 <option value="Genus">Genus</option>
76 <option value="Species">Species</option> 82 <option value="Species">Species</option>
77 </param> 83 </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)"> 84 -->
79 <option value="1">OTU</option> 85 <conditional name="plot_selection">
80 <option value="2" selected="true">SAMPLE</option> 86 <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)">
81 <option value="3">BIPLOT</option> 87 <option value="1">OTU</option>
82 <option value="4">SPLIT PLOT</option> 88 <option value="2" selected="true">SAMPLE</option>
83 </param> 89 <option value="3">BIPLOT</option>
90 <option value="4">SPLIT PLOT</option>
91 </param>
92 <when value="1">
93 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
94 <option value="Kingdom">Kingdom</option>
95 <option value="Phylum" selected="true">Phylum</option>
96 <option value="Class">Class</option>
97 <option value="Order">Order</option>
98 <option value="Family">Family</option>
99 <option value="Genus">Genus</option>
100 <option value="Species">Species</option>
101 </param>
102 </when>
103 <when value="2">
104 </when>
105 <when value="3">
106 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
107 <option value="Kingdom">Kingdom</option>
108 <option value="Phylum" selected="true">Phylum</option>
109 <option value="Class">Class</option>
110 <option value="Order">Order</option>
111 <option value="Family">Family</option>
112 <option value="Genus">Genus</option>
113 <option value="Species">Species</option>
114 </param>
115 </when>
116 <when value="4">
117 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
118 <option value="Kingdom">Kingdom</option>
119 <option value="Phylum" selected="true">Phylum</option>
120 <option value="Class">Class</option>
121 <option value="Order">Order</option>
122 <option value="Family">Family</option>
123 <option value="Genus">Genus</option>
124 <option value="Species">Species</option>
125 </param>
126 </when>
127 </conditional>
84 </inputs> 128 </inputs>
85 <outputs> 129 <outputs>
130 <data format="txt" name="log" label="${tool.name} - stress value - distance matrix - sample column sum"/>
86 <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/> 131 <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/>
87 </outputs> 132 </outputs>
88 133
89 <tests> 134 <tests>
90 <test> <!-- Test #1: Test BIOM format input --> 135 <test> <!-- Test #1: Test BIOM format input -->
112 </test> 157 </test>
113 </tests> 158 </tests>
114 159
115 <help> 160 <help>
116 **What it does** 161 **What it does**
117 Creates NMDS plot using R package called phyloseq_. 162 Creates various ordination plot using an R_package_called_phyloseq_,specifically according to the methods outlined in the Phyloseq_Ordination_Plot_Tutorial_.
118 163
119 .. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html 164 .. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html
165 .. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html
120 166
121 ----- 167 -----
122 168
123 **Input** 169 **Input**
124 170
125 - **Choose an input file type** - BIOM File or TABULAR file 171 - **Choose an input file type** - either 1 BIOM File or 3 TABULAR files (OTU, taxonomy and Metadata tables)
126 - **Select variable for ordination** - This column is used to extract unique value from the column of interest for ordination plot 172 - **Classify plot by** - points on the plot will be colour coded according to their value of the selected feature
127 - **OTU TABLE** - this is a OTU matrix 173 - **Select Ordination method** - several methods are supported
128 - **Taxonomy TABLE** - this is a TAX matrix 174 - **Select Distance method** - several methods are supported
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 175 - **Select a taxonomic rank for the analysis** - select a taxonomy for ordination plot
133 176
134 ----- 177 -----
135 178
136 ========= 179 =========