update XML files and test-data

galaxyproject · Oct 30, 2024 · c21c2b6 · c21c2b6
1 parent ad09a29
commit c21c2b6
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Showing 3 changed files with 15 additions and 8 deletions.
diff --git a/tools/ampvis2/alpha_diversity.xml b/tools/ampvis2/alpha_diversity.xml
@@ -13,22 +13,22 @@
             library(ampvis2, quietly = TRUE)
 
             d <- readRDS("$data")
-            a <- amp_alphadiv(d,
+            table <- amp_alphadiv(d,
                 measure = c($m),
                 richness = $richness
                 @RAREFY_TOKEN@,
             )
-            b <- amp_alphadiv(d,
+            plot <- amp_alphadiv(d,
                 measure = c($m),
                 richness = $richness
                 @RAREFY_TOKEN@,
                 plot = TRUE,
                 plot_group_by = "$group_by",
                 plot_scatter = $plot_scatter
             )
-            write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) 
+            write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) 
             ggsave("$alphadiv_plot",
-                    plot = b,
+                    plot = plot,
                     device = "$output_options.out_format"
                     #if str($output_options.plot_width) != ''
                         , width = $output_options.plot_width
@@ -55,7 +55,7 @@
     </inputs>
     <outputs>
         <data name="alphadiv" format="tabular"/>
-        <expand macro="out_macro" name="alphadiv_plot" label=": alpha diversity plot"/>
+        <expand macro="out_macro" name="alphadiv_plot" label=": plot"/>
     </outputs>
     <tests>
         <test>
@@ -71,7 +71,11 @@
                     <has_n_columns n="10"/>
                 </assert_contents>
             </output>
-            <output name="alphadiv_plot" value="AalborgWWTPs-alpha_diversity_plot.pdf" ftype="pdf" compare="sim_size"/>
+            <output name="alphadiv_plot" ftype="pdf">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
@@ -90,8 +94,11 @@
                     <has_text text="&#9;500&#9;"/>
                 </assert_contents>
             </output>
-            <output name="alphadiv_plot" value="AalborgWWTPs-alpha_diversity_plot2.pdf" ftype="pdf" compare="sim_size"/>
-
+            <output name="alphadiv_plot">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot.pdf b/tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot.pdf
diff --git a/tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot2.pdf b/tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot2.pdf