# HG changeset patch
# User bgruening
# Date 1666791455 0
# Node ID cb8dfd28c16f0daea4fac751167ca15799676fae
# Parent  276f5d8712d5b5104889bab04ab3ea97a0e601db
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193

diff -r 276f5d8712d5 -r cb8dfd28c16f flye.xml
--- a/flye.xml	Tue Nov 23 08:35:32 2021 +0000
+++ b/flye.xml	Wed Oct 26 13:37:35 2022 +0000
@@ -39,6 +39,7 @@
         #end if
         $meta
         $scaffold
+        $no_alt_contigs
     ]]></command>
     <inputs>
         <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
@@ -97,6 +98,7 @@
             </when>
             <when value="false" />
         </conditional>
+        <param argument="--no-alt-contigs" type="boolean" truevalue="--no-alt-contigs" falsevalue="" checked="false" label="Remove all non-primary contigs from the assembly"/>
         <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/>
     </inputs>
     <outputs>
@@ -321,6 +323,33 @@
                </assert_contents>
             </output>
         </test>
+        <!--Test 09: test not-alt-contigs parameter w-->
+        <test expect_num_outputs="4">
+            <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
+            <param name="mode" value="--nano-raw"/>
+            <param name="iterations" value="0"/>
+            <param name="no_alt_contigs" value="true"/>
+            <output name="assembly_info" ftype="tabular">
+                <assert_contents>
+                    <has_size value="151" delta="100"/>
+               </assert_contents>
+            </output>
+            <output name="assembly_graph" ftype="graph_dot">
+                <assert_contents>
+                    <has_size value="217" delta="100"/>
+               </assert_contents>
+            </output>
+            <output name="assembly_gfa" ftype="txt">
+                <assert_contents>
+                    <has_size value="5110" delta="100"/>
+               </assert_contents>
+            </output>
+            <output name="consensus" ftype="fasta">
+                <assert_contents>
+                    <has_size value="5123" delta="100"/>
+               </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r 276f5d8712d5 -r cb8dfd28c16f macros.xml
--- a/macros.xml	Tue Nov 23 08:35:32 2021 +0000
+++ b/macros.xml	Wed Oct 26 13:37:35 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.9</token>
+    <token name="@TOOL_VERSION@">2.9.1</token>
     <token name="@SUFFIX_VERSION@">0</token>
     <xml name="requirements">
         <requirements>