diff phyloseq_from_dada2.xml @ 2:87064cb77a52 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b

--- a/phyloseq_from_dada2.xml	Fri Feb 09 21:42:24 2024 +0000
+++ b/phyloseq_from_dada2.xml	Sat Mar 16 07:55:48 2024 +0000
@@ -9,11 +9,15 @@
 Rscript '${__tool_directory__}/phyloseq_from_dada2.R' 
 --sequence_table '$sequence_table' 
 --taxonomy_table '$taxonomy_table' 
+#if $sample_table
+    --sample_table '$sample_table' 
+#end if
 --output '$output'
     ]]></command>
     <inputs>
         <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/>
         <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/>
+        <param name="sample_table" type="data" format="tabular" optional="true" label="Sample table" help="Rows are sample names, Columns are properties"/>
     </inputs>
     <outputs>
         <data name="output" format="phyloseq"/>
@@ -22,7 +26,36 @@
         <test>
             <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
             <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
-            <output name="output" value="output.phyloseq" ftype="phyloseq" compare="sim_size"/>
+            <output name="output" ftype="phyloseq">
+                <assert_contents>
+                    <has_size value="4600" delta="400"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="phyloseq-class experiment-level object"/>
+                <has_text text="otu_table()   OTU Table:         [ 64 taxa and 2 samples ]"/>
+                <has_text text="tax_table()   Taxonomy Table:    [ 64 taxa by 6 taxonomic ranks ]"/>
+                <has_text text="refseq()      DNAStringSet:      [ 64 reference sequences ]"/>
+                <has_n_lines n="4"/>
+            </assert_stdout>
+        </test>
+        <test>
+            <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
+            <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
+            <param name="sample_table" value="sample_data.tabular" ftype="tabular"/>
+            <output name="output" ftype="phyloseq">
+                <assert_contents>
+                    <has_size value="4600" delta="400"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="phyloseq-class experiment-level object"/>
+                <has_line line="otu_table()   OTU Table:         [ 64 taxa and 2 samples ]"/>
+                <has_line line="sample_data() Sample Data:       [ 2 samples by 2 sample variables ]"/>
+                <has_line line="tax_table()   Taxonomy Table:    [ 64 taxa by 6 taxonomic ranks ]"/>
+                <has_line line="refseq()      DNAStringSet:      [ 64 reference sequences ]"/>
+                <has_n_lines n="5"/>
+            </assert_stdout>
         </test>
     </tests>
     <help>