--- a/discosnp_RAD.xml	Wed Jan 22 17:26:07 2020 -0500
+++ b/discosnp_RAD.xml	Mon Aug 17 10:37:37 2020 -0400
@@ -25,7 +25,13 @@
         run_discoSnpRad.sh
         @discosnp_inputs@
         -S "\$CONNECTOR_DIR"
+        --max_size_cluster ${max_size_cluster}
         -a ${a}
+        ${high_precision}
+        --max_missing ${max_missing}
+        --min_rank ${min_rank}
+
+        --max_threads \${GALAXY_SLOTS:-1}
 
   ]]></command>
 
@@ -33,20 +39,23 @@
 
       <expand macro="discosnp_inputs" />
 
-      <param argument="-b" type="select" label="Branching strategy">
-          <option value="1">forbid SNPs for wich the two paths are branching</option>
-          <option value="2">No limitation on branching</option>
-      </param>
+      <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="*_coherent_sorted_with_clusters.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
-      <data name="fasta" from_work_dir="discoRad_*_coherent.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
+      <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>
@@ -59,14 +68,22 @@
           <param name="P" value="4"/>
           <param name="k" value="31"/>
           <param name="b" value="2"/>
+          <param name="max_size_cluster" value="50"/>
+          <param name="max_missing" value="0.95"/>
+          <param name="min_rank" value="0.0"/>
           <output name="fasta" file="discosnpRAD/fasta.fa"/>
           <output name="vcf">
               <assert_contents>
-                  <has_n_lines n="8"/>
-                  <has_text text="Ty=SNP;Rk=0;UL=23;UR=39;CL=.;CR=.;Genome=.;Sd=."/>
+                  <has_n_lines n="31"/>
+                  <has_text text="Ty=SNP;Rk=0.0;UL=23;UR=39;CL=23;CR=39;Genome=.;Sd=.;Cluster=0;ClSize=2"/>
                   <has_text text="0/1:84:604,15,604:42,42:0,0"/>
               </assert_contents>
           </output>
+          <assert_command>
+              <has_text text="--max_size_cluster 50"/>
+              <has_text text="--max_missing 0.95"/>
+              <has_text text="--min_rank 0.0"/>
+          </assert_command>
       </test>
   </tests>