--- a/assembly_stats_txt.xml	Tue Nov 07 12:28:31 2017 -0500
+++ b/assembly_stats_txt.xml	Fri May 29 13:51:50 2020 -0400
@@ -1,23 +1,27 @@
-<tool id="assemblystats" name="assemblystats" version="1.0.1">
+<tool id="assemblystats" name="assemblystats" version="1.1.0">
 	<description>Summarise an assembly (e.g. N50 metrics)</description>
 	<requirements>
-		<requirement type="package" version="1.6.924">perl-bioperl</requirement>
-		<requirement type="package" version="5.0.4">gnuplot</requirement>
+		<requirement type="package" version="1.7.2">perl-bioperl</requirement>
+		<requirement type="package" version="5.2.7">gnuplot</requirement>
+		<requirement type="package" version="3.7.6">python</requirement>
 	</requirements>
 	<command detect_errors="exit_code"><![CDATA[
-		python $__tool_directory__/assembly_stats_txt.py 
+		python3 $__tool_directory__/assembly_stats_txt.py 
 
-		'$type' 
-		'$stats.extra_files_path'
-		'$type'
-		'$bucket'
-		'$input'
-		'$stats'
-		'$sortedcontigs'
-		'$histogrampng' 
-		'$summedcontigspng'
-		'$histogramdata' 
-		'$summedcontigdata' 
+		-d '$stats.extra_files_path'
+		-t '$type'
+		-i '$input'
+		-s '$stats'
+		-sc '$sortedcontigs'
+		-hpng '$histogrampng' 
+		-spng '$summedcontigspng'
+		-hd '$histogramdata' 
+		-scd '$summedcontigdata' 
+		
+		#if $bucket
+			-b
+		#end if
+
 		]]></command>
 		<inputs>
 			<param label="Type of read" name="type" type="select" help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)">
@@ -25,7 +29,7 @@
 				<option value="isotig">Isotig (if from transcriptomic assembly)</option>
 				<option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
 			</param>
-			<param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="-b" falsevalue="" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/>
+			<param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="true" falsevalue="false" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/>
 			<param format="fasta" name="input" type="data" label="Source file in FASTA format"/>
 			<param name = "all_outputs" type ="boolean" checked="false" label="Return all output files" help="If checked, all output files will be displayed. If not checked, only the file 'Assembly Statistics' will be provided." />
 		</inputs>