diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index 726e5120afc..e539c9ac1a7 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -39,8 +39,8 @@
     		<param name="minChainT" type="hidden" value="0" />
     	</when>
     	<when value="1">
-    	    <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/>
-    		<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/>
+    	    <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/>
+    		<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/>
     		<param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
     	</when>
 	</conditional>
diff --git a/tools/filters/bed2gff.xml b/tools/filters/bed2gff.xml
index 69070a4b100..f9e2128c3ba 100644
--- a/tools/filters/bed2gff.xml
+++ b/tools/filters/bed2gff.xml
@@ -2,7 +2,7 @@
   <description>converter</description>
   <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
   <inputs>
-    <param format="bed" name="input" type="data" label="Convert this query"/>
+    <param format="bed" name="input" type="data" label="Convert this dataset"/>
   </inputs>
   <outputs>
     <data format="gff" name="out_file1" />
diff --git a/tools/filters/condense_characters.xml b/tools/filters/condense_characters.xml
index eb06f75c6bf..c119720d31f 100644
--- a/tools/filters/condense_characters.xml
+++ b/tools/filters/condense_characters.xml
@@ -12,7 +12,7 @@
       <option value="U">Underscores</option>
       <option value="P">Pipes</option>
     </param>
-    <param format="txt" name="input" type="data" label="in this Query"/>
+    <param format="txt" name="input" type="data" label="in this Dataset"/>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input" />
diff --git a/tools/filters/convert_characters.xml b/tools/filters/convert_characters.xml
index e3c54afea43..032ff74d4f6 100644
--- a/tools/filters/convert_characters.xml
+++ b/tools/filters/convert_characters.xml
@@ -13,7 +13,7 @@
       <option value="P">Pipes</option>
       <option value="Co">Colons</option>
     </param>
-    <param format="txt" name="input" type="data" label="in Query"/>
+    <param format="txt" name="input" type="data" label="in Dataset"/>
   </inputs>
   <outputs>
     <data format="tabular" name="out_file1" />
diff --git a/tools/filters/gff2bed.xml b/tools/filters/gff2bed.xml
index fde5d380970..270ff023733 100644
--- a/tools/filters/gff2bed.xml
+++ b/tools/filters/gff2bed.xml
@@ -2,7 +2,7 @@
   <description>converter</description>
   <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
   <inputs>
-    <param format="gff" name="input" type="data" label="Convert this query"/>
+    <param format="gff" name="input" type="data" label="Convert this dataset"/>
   </inputs>
   <outputs>
     <data format="bed" name="out_file1" />
diff --git a/tools/filters/sorter.xml b/tools/filters/sorter.xml
index bd35d265017..e2fed1a4bae 100644
--- a/tools/filters/sorter.xml
+++ b/tools/filters/sorter.xml
@@ -14,7 +14,7 @@
       #end for
   </command>
   <inputs>
-    <param format="tabular" name="input" type="data" label="Sort Query" />
+    <param format="tabular" name="input" type="data" label="Sort Dataset" />
     <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/>
     <param name="style" type="select" label="with flavor">
       <option value="num">Numerical sort</option>
diff --git a/tools/new_operations/get_flanks.xml b/tools/new_operations/get_flanks.xml
index 3a9c29efcd6..2c4a0e5b852 100644
--- a/tools/new_operations/get_flanks.xml
+++ b/tools/new_operations/get_flanks.xml
@@ -50,11 +50,11 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel
 
 **Example 1**
 
-- For the following query::
+- For the following dataset::
 
    chr22  1000  7000  NM_174568 0 +
 
-- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::
+- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**::
 
    chr22  500  800  NM_174568 0 +
 
@@ -62,11 +62,11 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel
 
 **Example 2**
 
-- For the following query::
+- For the following dataset::
 
    chr22  1000  7000  NM_028946 0 -
 
-- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::
+- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::
 
    chr22  500  800  NM_028946 0 -
 
@@ -75,4 +75,4 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel
 </help>  
 
 
-</tool>
\ No newline at end of file
+</tool>