diff count-median.xml @ 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.