--- a/discosnp_RAD.xml	Mon Aug 17 10:37:37 2020 -0400
+++ b/discosnp_RAD.xml	Thu May 06 12:43:46 2021 +0000
@@ -1,27 +1,28 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@">
+<tool id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@">
     <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="discosnp_requirements" />
-    <command><![CDATA[
-        ## simple option
-        #if str( $input_type_options.input_type) == "single"
-            @discosnp_single_reads@
-        ## paired option
-        #else if str( $input_type_options.input_type) == "paired"
-            @discosnp_paired_reads@
-        ## mix option
+    <command detect_errors="exit_code"><![CDATA[
+        #if str($input_type_options.input_type) == "single"
+            @discosnp_single_for@
+            @single_reads@
+            @discosnp_single_end_for@
+        #else if str($input_type_options.input_type) == "paired"
+            @discosnp_paired_for@
+            @paired_reads@
+            @discosnp_paired_end_for@
         #else
-            @discosnp_single_reads@
-            @discosnp_paired_reads@
+            @discosnp_single_for@
+            @single_reads@
+            @discosnp_single_end_for@
+            @discosnp_paired_for@
+            @paired_reads@
+            @discosnp_paired_end_for@
         #end if
-
-        ## get the absolute path for short_reads_connector
         CONNECTOR_PATH=`which short_read_connector.sh` &&
         CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` &&
-
         run_discoSnpRad.sh
         @discosnp_inputs@
         -S "\$CONNECTOR_DIR"
@@ -30,39 +31,26 @@
         ${high_precision}
         --max_missing ${max_missing}
         --min_rank ${min_rank}
-
         --max_threads \${GALAXY_SLOTS:-1}
-
   ]]></command>
-
   <inputs>
-
       <expand macro="discosnp_inputs" />
-
       <param argument="--high_precision" type="boolean" checked="false" truevalue="--high_precision" falsevalue="" label="Lower recall / higher precision mode." help="With this parameter no symmetrical crossroads may be traversed during bubble detection (by default up to 5 symmetrical crossroads may be traversed during bubble detection)." />
-
       <param argument="-a" type="integer" label="Maximal size of ambiguity of INDELs" value="20" help="INDELS whose ambiguity is higher than this value are not output"/>
-
       <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/>
-
       <param argument="--max_missing" type="float" label="Remove variants with more than this proportion of missing values" value="0.95" help="Default 0.95, removes variants detected in 5% and less populations"/>
-
       <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
-
       <expand macro="discosnp_options" />
-
   </inputs>
-
   <outputs>
       <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
       <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
   </outputs>
-
   <tests>
       <test>
           <conditional name="input_type_options">
               <param name="input_type" value="single"/>
-              <param name="list_reads" value="discosnpRAD/loci_reads" ftype="fasta" />
+              <param name="list_reads" value="discosnpRAD/loci_reads.gz" ftype="fasta.gz" />
           </conditional>
           <param name="D" value="0"/>
           <param name="P" value="4"/>
@@ -86,7 +74,6 @@
           </assert_command>
       </test>
   </tests>
-
   <help><![CDATA[
 
 **Description**