--- a/abyss-pe.xml	Wed Dec 04 08:30:29 2019 -0500
+++ b/abyss-pe.xml	Fri Mar 19 21:37:30 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@">
+<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy1">
     <description>de novo sequence assembler</description>
     <macros>
         <token name="@TOOL_VERSION@">2.2.3</token>
@@ -10,14 +10,14 @@
                     <option value="paired_il">1 dataset of interleaved reads</option>
                 </param>
                 <when value="paired">
-                    <param name="reads1" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 1" />
-                    <param name="reads2" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 2" />
+                    <param name="reads1" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 1" />
+                    <param name="reads2" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 2" />
                 </when>
                 <when value="paired_collection">
                     <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />
                 </when>
                 <when value="paired_il">
-                    <param name="reads_il" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Interleaved paired-end reads" />
+                    <param name="reads_il" type="data" format="fasta,fastq,fastq.gz" label="Interleaved paired-end reads" />
                 </when>
             </conditional>
         </xml>
@@ -149,11 +149,11 @@
         <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
             <expand macro="reads_conditional" />
         </repeat>
-        <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" />
+        <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Single-end reads" />
         <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)">
             <expand macro="reads_conditional" />
         </repeat>
-        <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
+        <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
         <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" />
         <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" />
         <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" />
@@ -197,8 +197,8 @@
             <repeat name="lib_repeat">
                 <conditional name="reads">
                     <param name="reads_selector" value="paired" />
-                    <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq" />
-                    <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
+                    <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz" />
+                    <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
                 </conditional>
             </repeat>
             <param name="k" value="50" />
@@ -211,7 +211,7 @@
             <output name="stats" file="abyss-stats1.tab" />
         </test>
         <test>
-            <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
+            <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
             <param name="k" value="50" />
             <output name="unitigs" file="abyss-unitigs2.fa" />
             <output name="bubbles" file="empty_file.fasta" />
@@ -220,8 +220,8 @@
             <output name="stats" file="abyss-stats2.tab" />
         </test>
         <test>
-            <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
-            <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
+            <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
+            <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
             <param name="k" value="50" />
             <output name="unitigs" file="abyss-unitigs3.fa" />
             <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />