--- a/macros.xml	Mon Aug 17 10:39:09 2020 -0400
+++ b/macros.xml	Thu May 06 12:44:17 2021 +0000
@@ -1,34 +1,73 @@
 <macros>
     <token name="@DISCOSNP_VERSION@">2.5.4</token>
 
+    <token name="@PROFILE@">20.01</token>
+
     <xml name="discosnp_requirements">
         <requirements>
             <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
         </requirements>
     </xml>
 
-    <token name="@discosnp_single_reads@"><![CDATA[
-        #for $input in $input_type_options.list_reads
-            #set $filename = os.path.basename(str($input)) + "." + $input.ext
-            ln -sf '${input}' '${filename}' &&
+    <token name="@discosnp_single_for@"><![CDATA[
+        #for $input in $input_type_options.list_reads:
+    ]]></token>
+
+    <token name="@discosnp_single_end_for@"><![CDATA[
             echo '${filename}' >> input.lst &&
         #end for
     ]]></token>
 
-    <token name="@discosnp_paired_reads@"><![CDATA[
-        #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
+    <token name="@single_reads@"><![CDATA[
+        #import re
+        #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
+        #if $input.ext.startswith('fasta'):
+            #set filename = $base_filename + ".fasta"
+        #else:
+            #set filename = $base_filename + ".fastq"
+        #end if
+        #if $input.ext.endswith('.gz'):
+            gunzip -c '${input}' > '${filename}' &&
+        #else:
+            ln -sf '${input}' '${filename}' &&
+        #end if
+    ]]></token>
 
-            #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
-            ln -sf '${paired.forward}' '${filenameFWD}' &&
+    <token name="@discosnp_paired_for@"><![CDATA[
+        #for $i, $paired in enumerate($input_type_options.list_paired_reads):
+    ]]></token>
 
-            #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
-            ln -sf '${paired.reverse}' '${filenameREV}' &&
+    <token name="@discosnp_paired_end_for@"><![CDATA[
+            echo '${forward}' > "paired_${i}.lst" &&
+            echo '${reverse}' >> "paired_${i}.lst" &&
+            echo "paired_${i}.lst" >> input.lst &&
+        #end for
+    ]]></token>
 
-            echo '${filenameFWD}' > "paired_${i}.lst" &&
-            echo '${filenameREV}' >> "paired_${i}.lst" &&
-            echo "paired_${i}.lst" >> input.lst &&
+    <token name="@paired_reads@"><![CDATA[
+        #set $base_forward = re.sub('[^\w_]', '_', $paired.forward.element_identifier)
+        #if $paired.forward.ext.startswith('fasta'):
+            #set forward = $base_forward + ".fasta"
+        #else:
+            #set forward = $base_forward + ".fastq"
+        #end if
+        #if $paired.forward.ext.endswith('.gz'):
+            gunzip -c '$paired.forward' > '$forward' &&
+        #else:
+            ln -sf '${paired.forward}' '$forward' &&
+        #end if
 
-        #end for
+        #set $base_reverse = re.sub('[^\w_]', '_', $paired.reverse.element_identifier)
+        #if $paired.reverse.ext.startswith('fasta'):
+            #set reverse = $base_reverse + ".fasta"
+        #else:
+            #set reverse = $base_reverse + ".fastq"
+        #end if
+        #if $paired.reverse.ext.endswith('.gz'):
+            gunzip -c '$paired.reverse' > '$reverse' &&
+        #else:
+            ln -sf '${paired.reverse}' '$reverse' &&
+        #end if
     ]]></token>
 
     <xml name="discosnp_inputs">
@@ -39,14 +78,14 @@
                 <option value="mix">Both single and paired reads</option>
             </param>
             <when value="single">
-                <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
+                <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
             </when>
             <when value="paired">
-                <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
+                <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
             </when>
             <when value="mix">
-                <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
-                <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
+                <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
+                <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
             </when>
         </conditional>
     </xml>
@@ -97,8 +136,8 @@
     ]]></token>
 
     <xml name="lordec_inputs">
-        <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
-        <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
+        <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq,fastq.gz" multiple="true" label="Short read FASTA/Q files" />
+        <param argument="-i" type="data" format="fasta,fastq.gz,fastq,fastq.gz" label="Long read FASTA/Q file" help="PacBio reads files" />
         <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
         <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
     </xml>