--- a/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml	Wed Jul 17 01:53:11 2019 -0400
+++ b/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml	Tue Aug 13 07:40:25 2019 -0400
@@ -13,11 +13,14 @@
  --p-seed="$pseed"
 #end if
 
-#if $pncores:
- --p-n-cores=$pncores
+
+#set $pncores = '${GALAXY_SLOTS:-4}'
+#if str($pncores):
+--p-n-cores=$pncores
 #end if
 
-#if $pnruns:
+
+#if str($pnruns):
  --p-n-runs=$pnruns
 #end if
 
@@ -25,7 +28,7 @@
  --p-substitution-model=$psubstitutionmodel
 #end if
 
-#if $pbootstrapreplicates:
+#if str($pbootstrapreplicates):
  --p-bootstrap-replicates=$pbootstrapreplicates
 #end if
 
@@ -100,7 +103,6 @@
 	<inputs>
 		<param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data"/>
 		<param label="--p-seed: INTEGER        Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="True" type="integer"/>
-		<param label="--p-n-cores: INTEGER     The number of cores to use for parallel processing. Range(0, None)        Use '0' to let IQ-TREE automatically determine the optimal number of cores to use.         [default: 1]" name="pncores" optional="True" type="integer" min="0" value="1"/>
 		<param label="--p-n-runs: INTEGER      Number of indepedent runs. Multiple  independent Range(1, None)        runs (e.g. 10) can outperform a single run in terms of likelihood maximisation.             [default: 1]" name="pnruns" optional="True" type="integer" min="1" value="1"/>
 		<param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
 			<option selected="True" value="None">Selection is Optional</option>