diff stacks_denovomap.xml @ 4:998dfec32bde draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f

--- a/stacks_denovomap.xml	Sat Jun 25 17:28:47 2016 -0400
+++ b/stacks_denovomap.xml	Mon Sep 26 11:44:20 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.1">
+<tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0">
     <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
     <macros>
         <import>macros.xml</import>
@@ -127,8 +127,8 @@
             #end if
             -M $assembly_options.M
             -n $assembly_options.n
-            -t $assembly_options.t
-            -H $assembly_options.H
+            $assembly_options.t
+            $assembly_options.H
 
             ## Batch description
             -b 1
@@ -179,7 +179,7 @@
             <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
             <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
             <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
-            <param name="n" argument="-n" type="integer" value="1" label="specify the number of mismatches allowed between loci when building the catalog"/>
+            <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/>
 
             <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
             <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
@@ -531,4 +531,3 @@
     </help>
     <expand macro="citation" />
 </tool>
-