# HG changeset patch
# User iuc
# Date 1727963202 0
# Node ID 4d23ab83ea29affd46475b16c7fb461430675a40
# Parent  b1fe2ef3d2447d45748b774e6bb9c5de53b2d3c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997

diff -r b1fe2ef3d244 -r 4d23ab83ea29 macros.xml
--- a/macros.xml	Mon Jun 17 11:47:23 2024 +0000
+++ b/macros.xml	Thu Oct 03 13:46:42 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.0.0a3</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="bio_tools">
         <xrefs>
@@ -34,7 +34,7 @@
 #end if
 ]]>
     </token>
-    <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
+    <token name="@THREADS@">--threads "\${GALAXY_SLOTS:-4}"</token>
     <xml name="tableinputs">
         <conditional name="parameters">
             <param name="type" type="select" label="Advanced Parameters"
@@ -43,7 +43,7 @@
                 <option value="specific">Show</option>
             </param>
             <when value="simple">
-                <param argument="" name="tablesize" type="select" label="Sample Type" display="radio">
+                <param argument="--max-tablesize" name="tablesize" type="select" label="Sample Type" display="radio">
                     <option value="1e9" selected="true">Microbial Genome</option>
                     <option value="2e9">Animal Transcriptome</option>
                     <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
@@ -51,8 +51,8 @@
                 </param>
             </when>
             <when value="specific">
-                <param argument="--ksize" name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
-                <param argument="--n_tables" name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
+                <param argument="--ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
+                <param argument="--n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
                 <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
                     label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
             </when>
@@ -90,11 +90,13 @@
             help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." />
     </xml>
     <xml name="abundance-histogram-output">
-        <data name="output_histogram_filename" format="txt"
-            label="${tool.name} on ${on_string}: k-mer abundance histogram. The
-                columns are: (1) k-mer abundance, (2) k-mer count, (3)
-                cumulative count, (4) fraction of total distinct k-mers." />
+        <data name="output_histogram_filename" format="csv"
+            label="${tool.name} on ${on_string}: k-mer abundance histogram" />
     </xml>
+    <token name="@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@"><![CDATA[
+ The columns  of the k-mer abundance histogram are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers.
+]]></token>
+
     <xml name="output_sequences" token_extension="">
         <collection name="sequences" type="list">
             <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
diff -r b1fe2ef3d244 -r 4d23ab83ea29 normalize-by-median.xml
--- a/normalize-by-median.xml	Mon Jun 17 11:47:23 2024 +0000
+++ b/normalize-by-median.xml	Thu Oct 03 13:46:42 2024 +0000
@@ -1,10 +1,10 @@
 <tool id="khmer_normalize_by_median" name="khmer: Normalize By Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Filter reads using digital normalization via k-mer abundances</description>
-    <expand macro="bio_tools"/>
     <macros>
         <token name="@BINARY@">normalize-by-median.py</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version" />
@@ -49,18 +49,18 @@
             label="Optional k-mer countgraph"
             help="The inputs file(s) will be processed using the kmer counts in the specified k-mer countgraph file as a starting point." />
         <param argument="--savegraph" name="save_countgraph" type="boolean" label="Save the k-mer countgraph(s) in a file" help="" />
-        <param argument="--cutoff" name="cutoff" type="integer" min="1" value="20" label="Cutoff" help="" />
+        <param argument="--cutoff" type="integer" min="1" value="20" label="Cutoff" help="" />
         <expand macro="tableinputs" />
     </inputs>
     <outputs>
-        <data name="countgraph" format="oxlicg" label="${tool.name} k-mer countgraph">
+        <data name="countgraph" format="oxlicg" label="${tool.name} on ${on_string}: k-mer countgraph">
             <filter>save_countgraph == True</filter>
         </data>
-        <data name="report" format="txt" label="${tool.name} report" />
+        <data name="report" format="csv" label="${tool.name} on ${on_string}: report" />
         <expand macro="output_sequences" extension="keep"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputs" value="test-abund-read-2.fa" ftype="fasta"/>
             <param name="type" value="specific" />
             <param name="cutoff" value="1" />
@@ -74,7 +74,7 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputs" value="test-abund-read-2.fa.gz"  ftype="fasta.gz"/>
             <param name="type" value="specific" />
             <param name="cutoff" value="2" />
@@ -89,12 +89,13 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="inputs" value="test-abund-read-paired.fa" ftype="fasta"/>
             <param name="type" value="specific" />
             <param name="cutoff" value="1" />
             <param name="ksize" value="17" />
             <param name="paired" value="true" />
+            <param name="save_countgraph" value="true"/>
             <output name="report" file="normalize-by-median.paired.report.txt" />
             <output_collection name="sequences" type="list">
                 <element name="test-abund-read-paired.fa" ftype="fasta">
@@ -104,6 +105,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output name="countgraph">
+                <assert_contents>
+                    <has_size size="1k"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[