# HG changeset patch
# User iuc
# Date 1616188819 0
# Node ID ac3f621a9607bd7d7734c18e117c97d351fbe559
# Parent  6a1330b7a6f8b4d21220f2d85f03e800adee538e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"

diff -r 6a1330b7a6f8 -r ac3f621a9607 metaspades.xml
--- a/metaspades.xml	Fri Jan 15 12:28:05 2021 +0000
+++ b/metaspades.xml	Fri Mar 19 21:20:19 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="metaspades" name="metaSPAdes" version="3.9.0">
+<tool id="metaspades" name="metaSPAdes" version="3.9.0.1">
     <description>assembler for metagenomics datasets</description>
     <requirements>
         <requirement type="package" version="3.9.0">spades</requirement>
@@ -62,14 +62,14 @@
                     <option value="paired-collection">Paired List Collection</option>
                 </param>
                 <when value="separate">
-                    <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
-                    <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
+                    <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" />
+                    <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" />
                 </when>
                 <when value="interleaved">
-                    <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
+                    <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" />
                 </when>
                 <when value="paired-collection">
-                    <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq" collection_type="paired" help="FASTQ format" />
+                    <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" />
                 </when>
             </conditional>
         </repeat>
@@ -90,6 +90,15 @@
             <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
             <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
         </test>
+        <test>
+            <param name="sc" value="false" />
+            <param name="careful" value="false" />
+            <param name="kmers" value="33,55" />
+            <param name="lib_type" value="paired_end" />
+            <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" />
+            <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" />
+            <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r 6a1330b7a6f8 -r ac3f621a9607 test-data/ecoli_1K_1.fq.gz
Binary file test-data/ecoli_1K_1.fq.gz has changed
diff -r 6a1330b7a6f8 -r ac3f621a9607 test-data/ecoli_1K_2.fq.gz
Binary file test-data/ecoli_1K_2.fq.gz has changed