Mercurial > repos > cropgeeks > flapjack

changeset 3:0d040ceef479 draft

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Uploaded
author cropgeeks
date Mon, 20 Feb 2017 08:15:58 -0500
parents 62161f30a69a
children 8970bd921458
files flapjack/mabcstats.xml
diffstat 1 files changed, 2 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/flapjack/mabcstats.xml	Fri Feb 17 09:21:40 2017 -0500
+++ b/flapjack/mabcstats.xml	Mon Feb 20 08:15:58 2017 -0500
@@ -13,13 +13,13 @@
 				+ "   -output=<output_file>          (required output file)");-->
 
   <description>Run marker assisted backcrossing analysis on a dataset</description>
-  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats -map=$map -genotypes=$genotypes -qtls=$qtls -parent1=$parent1 -parent2=$parent2 -model=$model -coverage=$coverage $decimalEnglish -output=$output</command>
+  <command>java -Xmx$advanced_options.memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats -map=$map -genotypes=$genotypes -qtls=$qtls -parent1=$parent1 -parent2=$parent2 -model=$model -coverage=$coverage $advanced_options.decimalEnglish -output=$output</command>
   <inputs>
     <param format="fjmap" name="map" type="data" label="Flapjack map file"
 		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
 	<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
 		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
-	<param format="bam" name="qtls" type="data" label="Flapjack QTL file"
+	<param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
 		help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
 	<param name="parent1" type="integer" value="1" label="Index of recurrent parent"
 		help="The index of the recurrent parent in the genotype file"/>
@@ -32,16 +32,6 @@
 	</param>
 	<param name="coverage" type="integer" value="10" label="Maximum coverage of a marker"
 		help="The maximum length of genome a marker can represent"/>
-	<!--<param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
-            label="Use English-style decimal marks"
-            help="Process input data using '.' as the decimal separator (as opposed to ',')"/>
-	<param name="memory" type="select" label="Memory"
-		help="How much memory to use; larger files may require more memory">
-	  <option selected="true" value="64m">64MB</option>
-	  <option value="128m">128MB</option>
-	  <option value="256m">256MB</option>
-	</param>-->
-	
 	
 	<conditional name="advanced_options">
 		<param name="show_advanced" type="boolean" label="Show advanced options"