--- a/trips_create_annotation/trips_create_annotation.xml	Sun Apr 17 08:45:11 2022 +0000
+++ b/trips_create_annotation/trips_create_annotation.xml	Wed Apr 20 15:18:02 2022 +0000
@@ -7,11 +7,11 @@
         <requirement type="package" version="3.0.2">intervaltree</requirement>
 
     </requirements>
-    <command><![CDATA[
-        python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6}
-    ]]></command>
+    <command>
+        python $__tool_directory__/create_annotation_sqlite.py ${output1} ${input2} ${input3} ${input4} ${input5} ${input6} ${output1}
+    </command>
     <inputs>
-        <param name="input1" type="text" label="Transcriptome name" />
+        <param name="input1" type="text" label="Transcriptome name" help="This will be the outputs filename (No Spaces!)"/>
         <param name="input2" type="data" format="gff" label="Transcriptome Annotation file (GFF/GTF)" />
         <param name="input3" type="data" format="fasta" label="Transcriptome FASTA File" />
         <param name="input4" type="integer" value="0" label="Psuedo UTR length" help="This value will be added used to create UTRs of this length. This is useful when looking at transcriptomes without annotated UTRs"/>
@@ -35,7 +35,7 @@
     <help>
     **What it does**
 
-    Builds a custom transcirptome annoatation stored in sqlite format for you organism.
+    Builds a custom transcirptome annoatation stored in sqlite format for your organism.
     </help>
     <citations/>
 </tool>