# HG changeset patch
# User iuc
# Date 1616189907 0
# Node ID a8a278849c18fe9eb5f999ab71e192cae904f2e0
# Parent  03fd468e158f44925257ae8e10e06ce8f0c46c2b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"

diff -r 03fd468e158f -r a8a278849c18 rnaspades.xml
--- a/rnaspades.xml	Thu Jan 07 17:50:06 2021 +0000
+++ b/rnaspades.xml	Fri Mar 19 21:38:27 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="rnaspades" name="rnaSPAdes" version="3.9.0.1">
+<tool id="rnaspades" name="rnaSPAdes" version="3.9.0.2">
     <description>assembler for RNA-Seq data</description>
     <requirements>
         <requirement type="package" version="3.9.0">spades</requirement>
@@ -81,23 +81,23 @@
                         <option value="paired-collection">Paired List Collection</option>
                     </param>
                     <when value="separate">
-                        <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
-                        <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
+                        <param format="fastq,fastq.gz" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
+                        <param format="fastq,fastq.gz" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
                     </when>
                     <when value="interleaved">
-                        <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
+                        <param format="fastq,fastq.gz" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
                     </when>
                     <when value="unpaired">
-                        <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
+                        <param format="fastq,fastq.gz" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
                     </when>
                     <when value="paired-collection">
-                        <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
+                        <param collection_type="paired" format="fastq,fastq.gz" help="FASTQ format" label="Paired-end reads collection" name="fastq,fastq.gz_collection" optional="false" type="data_collection" />
                     </when>
                 </conditional>
             </repeat>
         </repeat>
-        <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
-        <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
+        <param optional="true" format="fasta,fastq,fastq.gz" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
+        <param optional="true" format="fasta,fastq,fastq.gz" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
     </inputs>
     <outputs>
         <data format="fasta" label="rnaSPAdes transcripts" name="output_transcripts" from_work_dir="transcripts.fasta" />
@@ -110,6 +110,13 @@
             <param name="rev_reads" value="rnaspades-in1-2.fq" ftype="fastq" />
             <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" />
         </test>
+        <test>
+            <param name="lib_type" value="paired_end" />
+            <param name="type" value="separate" />
+            <param name="fwd_reads" value="rnaspades-in1-1.fq.gz" ftype="fastq.gz" />
+            <param name="rev_reads" value="rnaspades-in1-2.fq.gz" ftype="fastq.gz" />
+            <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" />
+        </test>
     </tests>
     <help>
 **What it does**
diff -r 03fd468e158f -r a8a278849c18 test-data/rnaspades-in1-1.fq.gz
Binary file test-data/rnaspades-in1-1.fq.gz has changed
diff -r 03fd468e158f -r a8a278849c18 test-data/rnaspades-in1-2.fq.gz
Binary file test-data/rnaspades-in1-2.fq.gz has changed