changeset 10:570505540a7b draft default tip

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

--- a/count-median.xml	Mon Jun 17 11:47:05 2024 +0000
+++ b/count-median.xml	Thu Oct 03 13:47:04 2024 +0000
@@ -1,10 +1,10 @@
 <tool id="khmer_count_median" name="khmer: Count Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Count the median/avg k-mer abundance for each sequence</description>
-    <expand macro="bio_tools"/>
     <macros>
         <token name="@BINARY@">count-median.py</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version" />
@@ -21,7 +21,7 @@
         <expand macro="input_countgraph_filename" />
     </inputs>
     <outputs>
-        <data name="output_summary_filename" format="txt"
+        <data name="output_summary_filename" format="csv"
             label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
@@ -40,8 +40,8 @@
 Count the median/avg k-mer abundance for each sequence in the input file,
 based on the k-mer counts in the given k-mer countgraph. Can be used to
 estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The
-output file contains sequence id, median, average, stddev, and seq length;
-fields are separated by spaces. For khmer 1.x count-median.py will split
+output file contains sequence id, median, average, stddev, and seq length.
+For khmer 1.x count-median.py will split
 sequence names at the first space which means that some sequence formats (e.g.
 paired FASTQ in Casava 1.8 format) will yield uninformative names. Use
 `--csv` to fix this behavior.

--- a/macros.xml	Mon Jun 17 11:47:05 2024 +0000
+++ b/macros.xml	Thu Oct 03 13:47:04 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" />