diff macros.xml @ 60:fe697e0cb24a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty

--- a/macros.xml	Mon Aug 18 07:02:05 2014 -0400
+++ b/macros.xml	Tue Jul 07 11:59:39 2015 -0400
@@ -1,19 +1,20 @@
 <macros>
 	<xml name="requirements">
 		<requirements>
-			<!-- <requirement type="binary">@BINARY@</requirement> -->
-			<requirement type="package" version="1.1">khmer</requirement>
+			<requirement type="package" version="2.0rc1">khmer</requirement>
 		</requirements>
+	</xml>
+	<xml name="version">
 		<version_command>@BINARY@ --version</version_command>
 	</xml>
 	<token name="@TABLEPARAMS@">#if $parameters.type == "simple"
   --ksize=20
   --n_tables=4
-  --min-tablesize=$parameters.tablesize
+  --max-tablesize=$parameters.tablesize
 #else
   --ksize=$parameters.ksize
   --n_tables=$parameters.n_tables
-  --min-tablesize=$parameters.tablesize_specific
+  --max-tablesize="$parameters.tablesize_specific"
   #end if</token>
 	<token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
 	<xml name="tableinputs">
@@ -93,7 +94,7 @@
 	</xml>
 	<xml name="abundance-histogram-output">
                 <data   name="output_histogram_filename"
-                        format="text"
+                        format="txt"
                         label="${tool.name} k-mer abundance histogram. The
                         columns are: (1) k-mer abundance, (2) k-mer count, (3)
                         cumulative count, (4) fraction of total distinct
@@ -102,14 +103,14 @@
 	</xml>
 	<xml name="output_sequences">
                 <data   name="output"
-                        format="input"
+                        format_source="inputs"
                         label="${tool.name} processed nucleotide sequence file">
                         <discover_datasets pattern="__name__" directory="output" visible="true"/>
                 </data>
 	</xml>
 	<xml name="output_sequences_single">
                 <data   name="output"
-                        format="input"
+                        format_source="input_sequence_filename"
                         label="${tool.name} processed nucleotide sequence file" />
 	</xml>
 	<xml name="input_zero">
@@ -152,7 +153,6 @@
 	</xml>
 	<xml name="stdio">
 	<stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
 		<exit_code	range="1:"
 				level="fatal" />
 	</stdio>