diff discosnp_pp.xml @ 4:912d042e4f1e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"

--- a/discosnp_pp.xml	Wed Jan 22 17:31:42 2020 -0500
+++ b/discosnp_pp.xml	Mon Aug 17 10:39:36 2020 -0400
@@ -25,14 +25,15 @@
 
         run_discoSnp++.sh
         @discosnp_inputs@
-        ${t}
         ${T}
+        -b ${b}
         #if str($VCF_option.mapping) == 'reference'
             -G '${reference_file}'
-            -M ${VCF_option.M}
             ${VCF_option.R}
         #end if
 
+        --max_threads \${GALAXY_SLOTS:-1}
+
   ]]></command>
 
   <inputs>
@@ -48,7 +49,6 @@
 
       <expand macro="discosnp_options" />
 
-      <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" />
       <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
 
       <conditional name="VCF_option" >
@@ -59,7 +59,6 @@
           <when value="default"></when>
           <when value="reference">
               <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
-              <param argument="-M" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" />
               <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
           </when>
       </conditional>