# HG changeset patch
# User iuc
# Date 1658913996 0
# Node ID 45210df786b9235579a42bf21d18a19e4f9152d4
# Parent  280386b252a592502dcc37465b4a1dcef47bc55a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c

diff -r 280386b252a5 -r 45210df786b9 nonpareil.xml
--- a/nonpareil.xml	Sun Nov 05 11:40:13 2017 -0500
+++ b/nonpareil.xml	Wed Jul 27 09:26:36 2022 +0000
@@ -1,16 +1,18 @@
-<tool id="nonpareil" name="Nonpareil" version="@WRAPPER_VERSION@.0">
+<tool id="nonpareil" name="Nonpareil" version="@TOOL_VERSION@.1" profile="21.01">
     <description>to estimate average coverage and generate Nonpareil curves</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">3.1.1</token>
+        <token name="@TOOL_VERSION@">3.1.1</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@WRAPPER_VERSION@">nonpareil</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">nonpareil</requirement>
     </requirements>
     <version_command>nonpareil -V</version_command>
     <command detect_errors="exit_code">
 <![CDATA[
+ln -s '$input' input &&
+
 nonpareil
-    -s '$input'
+    -s input
     -T '$algo'
     #if $input.is_of_type("fasta")
         -f 'fasta'
@@ -44,6 +46,7 @@
         -x '$mating.proba'
     #end if
     -r '$seed'
+    && echo $log_test
     ]]></command>
     <inputs>
         <param name="input" type="data" format="fastq,fasta" label="Input sequences" help="FastQ format is recommended for kmer algorithm and Fasta for the alignment" argument="-s"/>
@@ -88,7 +91,7 @@
         <data format="tabular" name="mating_vector_output" label="${tool.name} on ${on_string}: Mates distribution"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="test.fasta"/>
             <param name="algo" value="alignment"/>
             <param name="subsampling" value="0.7"/>
@@ -119,7 +122,7 @@
             <output name="summary" value="test1-summary" compare="sim_size" delta="0"/>
             <output name="mating_vector_output" value="test1-mating_vector_output" compare="sim_size" delta="0"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="test.fastq"/>
             <param name="algo" value="kmer"/>
             <param name="subsampling" value="0.7"/>