Mercurial > repos > iuc > kmer2stats

changeset 1:6ae87ffcea01 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/kmer2stats/ commit 069a351be3e6272c2d511c545593f32fd18f8a84
author iuc
date Tue, 22 Apr 2025 11:34:36 +0000
parents a926baa751bf
children
files kmer2stats.xml
diffstat 1 files changed, 16 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/kmer2stats.xml	Wed Apr 16 09:35:15 2025 +0000
+++ b/kmer2stats.xml	Tue Apr 22 11:34:36 2025 +0000
@@ -1,8 +1,8 @@
 <tool id="kmer2stats" name="Kmer2Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
-    <description>A tool for creating data files for statistics based on kmers</description>
+    <description>A tool that computes kmer alpha diversity metrics and other statistics</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">kmer2stats</requirement>
@@ -19,24 +19,24 @@
         <param name="input_file" type="data" format="tabular,txt" label="File input"/> 
     </inputs>
     <outputs>
-        <data name="output_file" format="csv" label="${tool.name}: COMPUTED DIVERSITY"/>
+        <data name="output_file" format="tabular" label="${tool.name}: kmer statistics"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="input_file" ftype="txt" value="test_file.txt"/>
-            <output name="output_file" ftype="csv" value="compute_diversity.csv"/>
+            <output name="output_file" ftype="tabular" value="compute_diversity.csv"/>
         </test>
     </tests>
     <help>
     <![CDATA[
 
-        **What this do**
+        **What this tool does**
 
-        This tool calculates diversity based on counted kmers.
+        This tool calculates alpha diversity metrics and other statistics such as observed features based on counted kmers.
 
         **Input**
 
-        This tool was designed to use the output from jellyfish but it also can take a file which should look like this:
+        This tool was designed to use the output from jellyfish but it also can take any file that looks like this:
 
         ::
 
@@ -65,8 +65,15 @@
 
         **Output**
 
-        This will be a file where the alpha diversity is calculated and stored as a panda dataframe which then can be used for plotting.
-    
+        Two column table with metric name in the first column and value in second column.
+
+        ::
+
+         Metric	Value
+         shannon	3.0008343481203097
+         simpson_d	0.05166872360281036
+         pielou_e	0.9856502651904311
+
     ]]>
     </help>
     <citations>