Mercurial > repos > simon-gladman > phyloseq_ordination_plot
diff phyloseq_ordinate_plot.xml @ 1:52f009b255a1 draft default tip
Updated tool
| author | simon-gladman |
|---|---|
| date | Thu, 22 Nov 2018 07:07:27 -0500 |
| parents | ae9cd53b7760 |
| children |
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--- a/phyloseq_ordinate_plot.xml Wed Sep 05 02:07:22 2018 -0400 +++ b/phyloseq_ordinate_plot.xml Thu Nov 22 07:07:27 2018 -0500 @@ -20,10 +20,16 @@ --meta_table='$META_TABLE' --category='$file_source.category' #end if + #if str($plot_selection.plot_type) == "2": + --plottype='$plot_selection.plot_type' + --kingdom='null' + #else: + --plottype='$plot_selection.plot_type' + --kingdom='$plot_selection.kingdom_field' + #end if --method='$ord_method' --distance='$distance' - --kingdom='$kingdom_field' - --plottype='$plot_type' + --log='$log' --outdir="$htmlfile.files_path" --htmlfile='$htmlfile' ]]> @@ -37,7 +43,7 @@ </param> <when value="set_biom"> <param format="biom1" name="input" type="data" label="Input File"/> - <param name="subsetColumn" type="select" label="Select variable for ordination"> + <param name="subsetColumn" type="select" label="Classify plot by"> <options> <filter type="data_meta" ref="input" key="table_column_metadata_headers" /> </options> @@ -47,7 +53,7 @@ <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/> <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/> <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/> - <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Select variable for ordination"/> + <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Classify plot by"/> </when> </conditional> <param name="ord_method" type="select" display="radio" label="Select Ordination method"> @@ -66,7 +72,7 @@ <option value="unifrac">unifrac (unweighted UniFrac distance)</option> <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option> </param> - <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> +<!-- <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> <option value="Kingdom">Kingdom</option> <option value="Phylum" selected="true">Phylum</option> <option value="Class">Class</option> @@ -75,14 +81,53 @@ <option value="Genus">Genus</option> <option value="Species">Species</option> </param> - <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)"> - <option value="1">OTU</option> - <option value="2" selected="true">SAMPLE</option> - <option value="3">BIPLOT</option> - <option value="4">SPLIT PLOT</option> - </param> + --> + <conditional name="plot_selection"> + <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)"> + <option value="1">OTU</option> + <option value="2" selected="true">SAMPLE</option> + <option value="3">BIPLOT</option> + <option value="4">SPLIT PLOT</option> + </param> + <when value="1"> + <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> + <option value="Kingdom">Kingdom</option> + <option value="Phylum" selected="true">Phylum</option> + <option value="Class">Class</option> + <option value="Order">Order</option> + <option value="Family">Family</option> + <option value="Genus">Genus</option> + <option value="Species">Species</option> + </param> + </when> + <when value="2"> + </when> + <when value="3"> + <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> + <option value="Kingdom">Kingdom</option> + <option value="Phylum" selected="true">Phylum</option> + <option value="Class">Class</option> + <option value="Order">Order</option> + <option value="Family">Family</option> + <option value="Genus">Genus</option> + <option value="Species">Species</option> + </param> + </when> + <when value="4"> + <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> + <option value="Kingdom">Kingdom</option> + <option value="Phylum" selected="true">Phylum</option> + <option value="Class">Class</option> + <option value="Order">Order</option> + <option value="Family">Family</option> + <option value="Genus">Genus</option> + <option value="Species">Species</option> + </param> + </when> + </conditional> </inputs> <outputs> + <data format="txt" name="log" label="${tool.name} - stress value - distance matrix - sample column sum"/> <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/> </outputs> @@ -114,21 +159,19 @@ <help> **What it does** -Creates NMDS plot using R package called phyloseq_. +Creates various ordination plot using an R_package_called_phyloseq_,specifically according to the methods outlined in the Phyloseq_Ordination_Plot_Tutorial_. -.. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html +.. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html +.. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html ----- **Input** -- **Choose an input file type** - BIOM File or TABULAR file -- **Select variable for ordination** - This column is used to extract unique value from the column of interest for ordination plot -- **OTU TABLE** - this is a OTU matrix -- **Taxonomy TABLE** - this is a TAX matrix -- **Metadata TABLE** - this is a metadata file of the experiment design -- **Select Ordination method** - select ordination method -- **Select Distance method** - select distance method for ordination plot +- **Choose an input file type** - either 1 BIOM File or 3 TABULAR files (OTU, taxonomy and Metadata tables) +- **Classify plot by** - points on the plot will be colour coded according to their value of the selected feature +- **Select Ordination method** - several methods are supported +- **Select Distance method** - several methods are supported - **Select a taxonomic rank for the analysis** - select a taxonomy for ordination plot -----