--- a/kissplice.xml	Mon Aug 17 10:39:09 2020 -0400
+++ b/kissplice.xml	Thu May 06 12:44:17 2021 +0000
@@ -1,5 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="kissplice" name="KisSplice" version="2.4.0">
+<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@">
     <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
     <macros>
         <import>macros.xml</import>
@@ -8,17 +7,12 @@
         <requirement type="package" version="2.4.0p1">kissplice</requirement>
     </requirements>
     <version_command>kissplice --version</version_command>
-    <command><![CDATA[
-
-        ## prepare symlinks
+    <command detect_errors="exit_code"><![CDATA[
         #set $samples = ""
-
-        #for x in $list_reads
-            #set $filename = os.path.basename(str($x)) + "." + $x.ext
-            ln -sf '${x}' '${filename}' &&
+        #for input in $list_reads
+            @single_reads@
             #set $samples += " -r '" + $filename + "'"
         #end for
-
         kissplice
         $samples
         -k ${k}
@@ -26,11 +20,9 @@
         -C ${C}
         ${output_context}
         --counts ${counts}
-
     ]]></command>
     <inputs>
-
-        <param name='list_reads' argument="-r" multiple="true" format="fasta,fastq" type="data" label="Reads file" />
+        <param name='list_reads' argument="-r" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" type="data" label="Reads file" />
         <param argument="-k" type="integer" value="41" label="K-mer length" />
         <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
         <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
@@ -63,16 +55,14 @@
             <filter>output_option == 'all_files'</filter>
         </data>
     </outputs>
-
     <tests>
         <test>
-            <param name="list_reads" value="kissplice/reads1,kissplice/reads2" ftype="fasta" />
+            <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
             <param name="k" value="25"/>
             <param name="output_option" value="alternative_file" />
             <output name="type1" file="kissplice/alternative_splicing.fa"/>
         </test>
     </tests>
-
     <help><![CDATA[
 
 **Description**