Update ampvis2

tools/ampvis2/alpha_diversity.xml

@@ -1,4 +1,4 @@
-<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
+<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -42,7 +42,7 @@
     <inputs>
         <expand macro="rds_input_macro"/>
         <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included">
-            <option value="observed" selected="true">observed</option>
+            <option value="uniqueotus" selected="true">unique OTUs</option>
             <option value="shannon" selected="true">shannon</option>
             <option value="simpson" selected="true">simpson</option>
             <option value="invsimpson" selected="true">invsimpson</option>
@@ -79,18 +79,18 @@
         </test>
         <test>
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
-            <param name="measure" value="observed,shannon"/> 
+            <param name="measure" value="uniqueotus,shannon"/> 
             <param name="richness" value="true"/>
             <param name="rarefy" value="500"/>
             <param name="group_by" value="Plant"/>
             <param name="plot_scatter" value="true"/>
             <output name="alphadiv">
                 <assert_contents>
-                    <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson&#9;Chao1&#9;ACE"/>
+                    <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Chao1&#9;ACE"/>
                     <has_text text="16SAMP-536&#9;"/>
                     <has_text text="&#9;Aalborg West&#9;"/>
                     <has_n_lines n="68"/>
-                    <has_n_columns n="13"/>
+                    <has_n_columns n="11"/>
                     <has_text text="&#9;500&#9;"/>
                 </assert_contents>
             </output>

tools/ampvis2/boxplot.xml

@@ -79,7 +79,9 @@
             <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
             <param name="group_by" value="Plant"/>
             <param name="sort_by" value="sum"/>
-            <param name="tax_show" value="5"/>
+            <conditional name="tax_show_cond">
+                <param name="tax_show" value="5"/>
+            </conditional>
             <param name="plot_flip" value="true"/>
             <param name="plot_log" value="true"/>
             <param name="adjust_zero" value="100000"/>

tools/ampvis2/export_otu.xml

@@ -1,4 +1,4 @@
-<tool id="ampvis2_export_otu" name="ampvis2 export otu" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
+<tool id="ampvis2_export_otu" name="ampvis2 export otu" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>

tools/ampvis2/frequency.xml

@@ -13,10 +13,9 @@
             data <- readRDS("$data")
             plot <- amp_frequency(
                 data,
-                ## https://github.com/KasperSkytte/ampvis2/issues/167
-                ## #if $group_by
-                ##     group_by = "$group_by",
-                ## #end if
+                #if $group_by
+                    group_by = "$group_by",
+                #end if
                 ## tax_class = NULL,
                 tax_empty = "$tax_empty",
                 tax_aggregate = "$tax_aggregate",
@@ -30,8 +29,7 @@
     </configfiles>
     <inputs>
         <expand macro="rds_metadata_input_macro"/>
-        <!-- https://github.com/KasperSkytte/ampvis2/issues/167
-            <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> -->
+        <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/>
         <expand macro="tax_empty_macro"/>
         <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
             <option value="OTU" selected="true">OTU/ASV</option>
@@ -50,13 +48,12 @@
             <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf" compare="sim_size"/>
         </test>
         <!-- group_by -->
-        <!-- https://github.com/KasperSkytte/ampvis2/issues/167
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
             <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
-            <param name="group_by" value="Plant"/> 
-            <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/>
-        </test> -->
+            <param name="group_by" value="Period"/> 
+            <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 What it does

tools/ampvis2/heatmap.xml

@@ -1,4 +1,4 @@
-<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
+<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -37,9 +37,13 @@
                 showRemainingTaxa = $showRemainingTaxa,
                 ## tax_class = NULL,
                 tax_empty = "$tax_empty",
-                ## TODO giving the order of the columns is difficult but "cluster" would be nice I guess
-                ## order_x_by = NULL,
-                ## order_y_by = NULL,
+                ## TODO giving the order of the columns is difficult, currently only "cluster"
+                #if $order_x_by
+                    order_x_by = "$order_x_by",
+                #end if
+                #if $order_y_by
+                    order_y_by = "$order_y_by",
+                #end if
                 plot_values = $plot_values_cond.plot_values,
                 #if $plot_values_cond.plot_values == "TRUE"
                     plot_values_size = $plot_values_cond.plot_values_size,
@@ -57,8 +61,10 @@
                 #if $sort_by_cond.sort_by_sel != 'no'
                     sort_by = "$sort_by_cond.sort_by",
                 #end if
-                #if $normalise_by
-                    normalise_by = "$normalise_by",
+                #if $normalise_by_cond.normalise_by_sel == "no"
+                    normalise_by = NULL,
+                #else
+                    normalise_by = "$normalise_by_cond.normalise_by",
                 #end if
                 #if $scale_by
                     scale_by = "$scale_by",
@@ -92,13 +98,43 @@
         <expand macro="metadata_select_discrete" argument="group_by" label="Group samples" help="By a categorical variable in the metadata"/>
         <expand macro="metadata_select_discrete" argument="facet_by" label="Facet the samples" help="By a categorical variable in the metadata."/>
         <expand macro="normalise_macro" checked="true"/>
+        <conditional name="normalise_by_cond">
+            <param name="normalise_by_sel" type="select">
+                <option value="no">No</option>
+                <option value="variable">Metadata variable</option>
+                <option value="sample">Specific sample</option>
+            </param>
+            <when value="no"/>
+            <when value="variable">
+                <param argument="normalise_by" type="select" optional="false" label="Metadata value" help="In order to select values a metadata list needs to be selected first. And group_by needs to be selected">
+                    <options from_dataset="metadata_list">
+                        <column name="name" index="1"/>
+                        <column name="value" index="1"/>
+                        <filter type="param_value" column="0" ref="group_by"/>
+                        <filter type="unique_value" column="1"/>
+                    </options>
+                </param>
+            </when>
+            <when value="sample">
+                <param argument="normalise_by" type="select" optional="false">
+                    <options from_dataset="metadata_list">
+                        <column name="name" index="1"/>
+                        <column name="value" index="1"/>
+                        <filter type="static_value" value="TRUE" column="2"/>
+                        <filter type="unique_value" column="1"/>
+                    </options>
+                </param>
+            </when>
+        </conditional>
         <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
             <option value="Phylum" selected="true">Phylum</option>
         </expand>
         <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/>
         <expand macro="tax_show_macro" value="10"/>
         <param argument="showRemainingTaxa" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Display sum of remaining taxa" help="Add an additional row at the bottom displaying the sum of all remaining taxa that are not part of the top tax_show most abundant taxa."/>
         <expand macro="tax_empty_macro"/>
+        <param argument="order_x_by" type="boolean" truevalue="cluster" falsevalue="" checked="false" label="hierarchical clustering of X axis"/>
+        <param argument="order_y_by" type="boolean" truevalue="cluster" falsevalue="" checked="false" label="hierarchical clustering of Y axis"/>
         <conditional name="plot_values_cond">
             <param argument="plot_values" type="select" label="Plot the values on the heatmap">
                 <option value="TRUE">Yes</option>
@@ -152,9 +188,6 @@
         </conditional>
         <param argument="color_palette_start" type="color" label="Start color for the heatmap" help="Choose the start color for the heatmap."/>
         <param argument="color_palette_end" type="color" label="End color for the heatmap" help="Choose the end color for the heatmap."/>
-        <!-- https://github.com/KasperSkytte/ampvis2/issues/168 
-            if this is possible again reuse: metadata_sample_or_variable_select ? -->
-        <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
         <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>
 
         <conditional name="plot_functions_cond">
@@ -218,9 +251,19 @@
             <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
             <param name="group_by" value="Plant"/>
             <param name="facet_by" value="Year"/>
-            <param name="out_format" value="tabular"/>
+            <section name="output_options">
+                <param name="out_format" value="tabular"/>
+            </section>
             <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.tsv" ftype="tabular"/>
         </test>
+        <!-- order_*_by: cluster -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="order_x_by" value="true"/>
+            <param name="order_y_by" value="true"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-order-by-cluster.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
+
         <!-- normalise -->
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
@@ -230,29 +273,33 @@
         <!-- normalise by a specific sample -->
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
-            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
-            <param name="normalise" value="true"/>
-            <param name="normalise_by" value="16SAMP-747"/>
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
+            <conditional name="normalise_by_cond">
+                <param name="normalise_by_sel" value="sample"/>
+                <param name="normalise_by" value="16SAMP-747"/>
+            </conditional>
             <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf" compare="sim_size"/>
         </test>
-        <!-- normalise by a metadata variable
-            https://github.com/KasperSkytte/ampvis2/issues/168 -->
-        <!-- <test expect_num_outputs="1">
+        <!-- normalise by a metadata variable -->
+        <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
             <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
             <param name="group_by" value="Plant"/>
             <conditional name="normalise_by_cond">
                 <param name="normalise_by_sel" value="variable"/>
-                <param name="normalise_by" value="Plant"/>
+                <param name="normalise_by" value="Aalborg West"/>
             </conditional>
             <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_variable.pdf" ftype="pdf"/>
-        </test> -->
+        </test>
         <!-- tax options -->
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
             <param name="tax_aggregate" value="Order"/>
             <param name="tax_add" value="Class"/>
-            <param name="tax_show" value="5"/>
+            <conditional name="tax_show_cond">
+                <param name="tax_show_sel" value="number"/>
+                <param name="tax_show" value="5"/>
+            </conditional>
             <param name="showRemainingTaxa" value="true"/>
             <output name="plot" value="AalborgWWTPs-heatmap-tax.pdf" ftype="pdf" compare="sim_size"/>
         </test>
@@ -299,14 +346,14 @@
         <!-- test with different color palettes -->
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
-            <param name="color_palette_start" value="red"/>
-            <param name="color_palette_end" value="yellow"/>
+            <param name="color_palette_start" value="#ff0000"/>
+            <param name="color_palette_end" value="#ffff00"/>
             <output name="plot" value="AalborgWWTPs-heatmap-red-yellow.pdf" ftype="pdf" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
-            <param name="color_palette_start" value="blue"/>
-            <param name="color_palette_end" value="green"/>
+            <param name="color_palette_start" value="#0000ff"/>
+            <param name="color_palette_end" value="#00ff00"/>
             <output name="plot" value="AalborgWWTPs-heatmap-blue-green.pdf" ftype="pdf" compare="sim_size"/>
         </test>