diff macros.xml @ 3:45ea720bba74 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6

--- a/macros.xml	Mon Dec 18 09:42:04 2023 +0000
+++ b/macros.xml	Mon Feb 26 07:55:49 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.7.22</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.8.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="header">
         <xrefs>
@@ -8,7 +8,8 @@
         </xrefs>
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>
-            <requirement type="package" version="2.1.1">r-readr</requirement>
+            <requirement type="package" version="2.1.5">r-readr</requirement>
+            <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement>
         </requirements>
         <version_command><![CDATA[
 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
@@ -36,7 +37,7 @@
     <token name="@SAVE_TAX_LIST@"><![CDATA[
                 for(level in colnames(data\$tax)){
                     for(u in unique(data\$tax[level])){
-                        write(u, file="$taxonomy_list_out", append=T)
+                        write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T)
                     }
                 }
     ]]></token>
@@ -152,7 +153,20 @@
         </expand>
     </xml>
 
+    <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by
+         sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168
+         leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) -->
     <xml name="metadata_sample_select" token_argument="">
+        <param argument="@ARGUMENT@" type="select" optional="true">
+            <options from_dataset="metadata_list">
+                <column name="name" index="1"/>
+                <column name="value" index="1"/>
+                <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
+                <filter type="unique_value" column="1"/>
+            </options>
+        </param>
+    </xml>
+    <xml name="metadata_sample_or_variable_select" token_argument="">
         <conditional name="@ARGUMENT@_cond">
             <param name="@ARGUMENT@_sel" type="select">
                 <option value="no">No</option>
@@ -164,14 +178,7 @@
                 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
             </when>
             <when value="sample">
-                <param argument="@ARGUMENT@" type="select" optional="true">
-                    <options from_dataset="metadata_list">
-                        <column name="name" index="1"/>
-                        <column name="value" index="1"/>
-                        <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
-                        <filter type="unique_value" column="1"/>
-                    </options>
-                </param>
+                <expand macro="metadata_sample_select"/>
             </when>
         </conditional>
     </xml>