diff abundance-dist-single.xml @ 10:65b382bf9b7c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997

--- a/abundance-dist-single.xml	Mon Jun 17 11:47:33 2024 +0000
+++ b/abundance-dist-single.xml	Thu Oct 03 13:47:14 2024 +0000
@@ -2,11 +2,11 @@
     <description>
         Calculate abundance distribution of k-mers
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <token name="@BINARY@">abundance-dist-single.py</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version" />
@@ -35,27 +35,27 @@
         <expand macro="tableinputs" />
     </inputs>
     <outputs>
-        <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} on ${on_string} k-mer countgraph">
+        <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} on ${on_string}: k-mer countgraph">
             <filter>save_countgraph == True</filter>
         </data>
         <expand macro="abundance-histogram-output" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_sequence_filename" value="test-abund-read-2.fa" />
             <param name="type" value="specific" />
             <param name="tablesize_specific" value="1e7" />
             <param name="n_tables" value="2" />
             <param name="ksize" value="17" />
             <param name="no_zero" value="false" />
-            <output name="output_histogram_filename" ftype="txt">
+            <output name="output_histogram_filename" ftype="csv">
                 <assert_contents>
                     <has_text text="1,96,96,0.98" />
                     <has_text text="1001,2,98,1.0" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_sequence_filename" value="test-abund-read-2.fq.gz" />
             <param name="type" value="specific" />
             <param name="tablesize_specific" value="1e7" />
@@ -63,12 +63,18 @@
             <param name="ksize" value="17" />
             <param name="no_zero" value="false" />
             <param name="bigcount" value="false" />
-            <output name="output_histogram_filename" ftype="txt">
+            <param name="save_countgraph" value="true"/>
+            <output name="output_histogram_filename" ftype="csv">
                 <assert_contents>
                     <has_text text="1,96,96,0.98" />
                     <has_text text="255,2,98,1.0" />
                 </assert_contents>
             </output>
+            <output name="optional_output_countgraph">
+                <assert_contents>
+                    <has_size size="1k"/>
+                </assert_contents>
+            </output>
         </test>
 
     </tests>
@@ -80,6 +86,7 @@
 `-b` will be about 1.15x the product of the `-x` and
 `-N` numbers.
 
+@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@
 
 @HELP_FOOTER@
 ]]>