diff transit_gumbel.xml @ 3:ecce0cbe659f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"

--- a/transit_gumbel.xml	Tue Oct 08 08:24:12 2019 -0400
+++ b/transit_gumbel.xml	Wed Oct 16 04:32:08 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="transit_gumbel" name="Gumbel" version="@VERSION@+galaxy1">
+<tool id="transit_gumbel" name="Gumbel" version="@VERSION@+galaxy2">
     <description>- determine essential genes</description>
     <macros>
         <import>macros.xml</import>
@@ -14,6 +14,7 @@
     </command>
     <inputs>
         <expand macro="standard_inputs">
+            <expand macro="handle_replicates" />
             <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
             <param name="burnin" argument="-b" type="integer" value="500" label="Number of Burn-in samples" />
             <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" />
@@ -68,7 +69,7 @@
        -b <integer>    :=  Number of Burn-in samples. Default -b 500
        -m <integer>    :=  Smallest read-count to consider. Default: -m 1
        -t <integer>    :=  Trims all but every t-th value. Default: -t 1
-       -r <string>     :=  How to handle replicates. Sum or Mean. Default: -r Sum
+       -r <string>     :=  How to handle replicates. Sum or Mean. Default: -r Mean
        --iN <float>     :=  Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
        --iC <float>     :=  Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
        -n <string>      := Determines which normalization method to use. Default -n TTR