Update ampvis2

tools/ampvis2/alpha_diversity.xml

@@ -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/heatmap.xml

@@ -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,
@@ -99,6 +103,8 @@
         <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>
@@ -221,6 +227,14 @@
             <param name="out_format" value="tabular"/>
             <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"/> 

tools/ampvis2/load.xml

@@ -8,9 +8,6 @@
         #if $otutable.is_of_type("biom1") or $otutable.is_of_type("biom2")
             ln -s '$otutable' otutable.biom &&
         #else if not $otutable.is_of_type("phyloseq")
-            ## asv/otu column can not be specified so set the needed name
-            ## if empty https://github.com/KasperSkytte/ampvis2/issues/166 
-            ## also done in taxonomy.tsv
             #if $asv_otu_col_empty
                 sed -e '1 s/^\t/ASV\t/' '$otutable' > otutable.tsv &&
             #else
@@ -71,6 +68,12 @@
                 #if $tree
                     tree = "$tree",
                 #end if
+                #if $otutable_OTUcolname
+                    otutable_OTUcolname = c("$otutable_OTUcolname"),
+                #end if
+                #if $taxonomy_OTUcolname
+                    taxonomy_OTUcolname = c("$taxonomy_OTUcolname"),
+                #end if
                 pruneSingletons = $pruneSingletons
             )
 
@@ -103,7 +106,6 @@
     </configfiles>
     <inputs>
         <param argument="otutable" type="data" format="phyloseq,dada2_sequencetable,tabular,biom1,biom2" label="OTU table"/>
-        <param name="asv_otu_col_empty" type="boolean" checked="false" label="OTU/ASV column has empty header" help="By default ampvis2 expects a column named ASV or OTU containing the ASV or OTU identifiers. By checking this a column with an empty header will be used (as produced by dada2)."/>
         <param name="asv_sequences" type="boolean" checked="false" label="ASV identifiers are the ASV sequences" help="By checking this the identifiers will be renamed to ASV1, ASV2, etc and the sequences will be stored in the ampvis2 object." />
         <param argument="metadata" type="data" format="tabular,tsv" optional="true" label="Sample metadata">
             <validator type="expression" message="Table must have at least 1 column"><![CDATA[value.metadata.columns > 0]]></validator>
@@ -117,6 +119,9 @@
             <option value="tax" selected="true">Taxonomy list</option>
             <option value="metadata" selected="true">Metadata list</option>
         </param>
+        <param name="asv_otu_col_empty" type="boolean" checked="false" label="Replace empty OTU/ASV column header by 'ASV'" help="By default ampvis2 expects a column named ASV, OTU, or #OTU ID containing the ASV or OTU identifiers. By checking this a column with an empty header will be set to ASV."/>
+        <param name="otutable_OTUcolname" type="text" value="" label="Name of the OTU column in the OTU table" help="By default a column named OTU, ASV, and #OTU ID is used"/>
+        <param name="taxonomy_OTUcolname" type="text" value="" label="Name of the OTU column in the taxonomy table" help="By default a column named OTU, ASV, and #OTU ID is used"/>
     </inputs>
     <outputs>
         <data name="ampvis" format="ampvis2"/>
@@ -258,6 +263,40 @@
                 <has_text text="232(100%)   232(100%)   232(100%) 231(99.57%) 209(90.09%) 127(54.74%)"/>
             </assert_stdout>
         </test>
+        <!-- load dada2 table with custom header -->
+        <test expect_num_outputs="3">
+            <param name="otutable" value="dada2-removeBimeraDenovo_custom.tab" ftype="dada2_sequencetable"/>
+            <param name="metadata" value="dada2-metadata.tsv" ftype="tsv"/>
+            <param name="taxonomy" value="dada2-assignTaxonomy_custom.tabular"/>
+            <param name="otutable_OTUcolname" value="custom"/>
+            <param name="taxonomy_OTUcolname" value="custom2"/>
+            <param name="asv_sequences" value="true"/>
+            <output name="ampvis" ftype="ampvis2">
+                <assert_contents>
+                    <has_size min="100" delta="2"/>
+                </assert_contents>
+            </output>
+            <output name="metadata_list_out">
+                <assert_contents>
+                    <has_n_lines n="23"/>
+                    <has_n_columns n="4"/>
+                    <has_text text="Sample"/>
+                </assert_contents>
+            </output>
+            <output name="taxonomy_list_out">
+                <assert_contents>
+                    <has_n_lines n="370"/>
+                    <has_n_columns n="2"/>
+                    <has_line line="Bacteria&#009;Kingdom"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="ampvis2 object with 4 elements."/> <!-- this also has fasta, i.e. 4 -->
+                <has_text text="6212.45"/>
+                <has_text text="Sample, time"/>
+                <has_text text="232(100%)   232(100%)   232(100%) 231(99.57%) 209(90.09%) 127(54.74%)"/>
+            </assert_stdout>
+        </test>
         <!-- load data from phyloseq -->
         <test expect_num_outputs="3">
             <param name="otutable" value="output.phyloseq" ftype="phyloseq"/>

tools/ampvis2/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.8.11</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="header">
         <xrefs>