diff macros.xml @ 59:08a599cf71d0

Bjoern's suggestions

--- a/macros.xml	Wed Aug 06 18:32:24 2014 -0400
+++ b/macros.xml	Mon Aug 18 07:02:05 2014 -0400
@@ -15,7 +15,7 @@
   --n_tables=$parameters.n_tables
   --min-tablesize=$parameters.tablesize_specific
   #end if</token>
-	<token name="@THREADS@">--threads \$GALAXY_SLOTS</token>
+	<token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
 	<xml name="tableinputs">
 		<conditional name="parameters">
 			<param	name="type"
@@ -43,7 +43,8 @@
 						Animal Transcriptome
 					</option>
 					<option value="4e9">
-						Small Animal Genome or Low-Diversity Metagenome
+						Small Animal Genome or
+						Low-Diversity Metagenome
 					</option>
 					<option value="16e9">
 						Large Animal Genome
@@ -117,7 +118,7 @@
                         truevalue=""
                         falsevalue="--no-zero"
                         checked="true" 
-                        help="Output zero count bins" />
+                        help="Output zero count bins (--no-zero)" />
 	</xml>
 	<xml name="software-citation">
 		<citation type="bibtex">@article{khmer2014,
@@ -149,5 +150,11 @@
 	<xml name="counting-citation">
 		<citation type="doi">10.1371/journal.pone.0101271</citation>
 	</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>
+	</xml>
 </macros>