--- a/monocle3-macros.xml	Mon Sep 16 09:50:29 2019 -0400
+++ b/monocle3-macros.xml	Wed Jan 29 10:38:23 2020 -0500
@@ -1,9 +1,11 @@
 <macros>
-  <token name="@TOOL_VERSION@">0.1.2</token>
+  <token name="@TOOL_VERSION@">0.1.3</token>
   <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.
+
 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
     ]]></token>
   <token name="@INPUT_OPTS@">
@@ -23,7 +25,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.0.3">monocle3-cli</requirement>
+      <requirement type="package" version="0.0.5">monocle3-cli</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -57,7 +59,7 @@
     </param>
     <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
   </xml>
-  
+
   <xml name="verbose_flag">
   	<param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
   </xml>

--- a/monocle3-preprocess.xml	Mon Sep 16 09:50:29 2019 -0400
+++ b/monocle3-preprocess.xml	Wed Jan 29 10:38:23 2020 -0500
@@ -16,7 +16,7 @@
     --use-genes '${use_genes}'
 #end if
 #if $residual_model_formula_str
-    --residual-model-formula-str '~${residual_model_formula_str}'
+    --residual-model-formula-str '${residual_model_formula_str}'
 #end if
 #if $pseudo_count
     --pseudo-count '${pseudo_count}'
@@ -44,7 +44,11 @@
       <option value="size_only">Size factor correction only</option>
     </param>
     <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/>
-    <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data (excluding the leading ~)."/>
+    <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data.">
+      <sanitizer>
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
     <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/>
     <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/>
     <expand macro="verbose_flag"/>