diff --git a/tools/fastq/fastq_masker_by_quality.xml b/tools/fastq/fastq_masker_by_quality.xml
index c4571099789..7e2d57a32c2 100644
--- a/tools/fastq/fastq_masker_by_quality.xml
+++ b/tools/fastq/fastq_masker_by_quality.xml
@@ -21,7 +21,7 @@
       <option value="ge">Greater than</option>
       <option value="gt">Greater than or equal</option>
     </param>
-    <param name="quality_score" type="integer" value="0"/>
+    <param name="quality_score" type="integer" value="0" label="Quality score"/>
   </inputs>
   <outputs>
     <data name="output_file" format="fastqsanger" />
diff --git a/tools/fastx_toolkit/fastq_quality_filter.xml b/tools/fastx_toolkit/fastq_quality_filter.xml
index af8766a5506..f60fe110b5f 100644
--- a/tools/fastx_toolkit/fastq_quality_filter.xml
+++ b/tools/fastx_toolkit/fastq_quality_filter.xml
@@ -2,7 +2,11 @@
 	<description></description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 
-	<command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command>
+	<command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 
 	<inputs>
 		<param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" />
@@ -19,14 +23,14 @@
 	<tests>
 		<test>
 			<!-- Test1:  100% of bases with quality 33 or higher (pretty steep requirement...) -->
-			<param name="input" value="fastq_qual_filter1.fastq" />
+			<param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" />
 			<param name="quality" value="33"/>
 			<param name="percent" value="100"/>
 			<output name="output" file="fastq_qual_filter1a.out" />
 		</test>
 		<test>
 			<!-- Test2:  80% of bases with quality 20 or higher -->
-			<param name="input" value="fastq_qual_filter1.fastq" />
+			<param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/>
 			<param name="quality" value="20"/>
 			<param name="percent" value="80"/>
 			<output name="output" file="fastq_qual_filter1b.out" />
diff --git a/tools/fastx_toolkit/fastq_to_fasta.xml b/tools/fastx_toolkit/fastq_to_fasta.xml
index 3b0dcb9283a..b391d0a5580 100644
--- a/tools/fastx_toolkit/fastq_to_fasta.xml
+++ b/tools/fastx_toolkit/fastq_to_fasta.xml
@@ -1,10 +1,14 @@
 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
 	<description>converter</description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
-	<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command>
+	<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v 
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 
 	<inputs>
-		<param format="fastq" name="input" type="data" label="FASTQ Library to convert" />
+		<param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
 
 		<param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
 			<option value="">yes</option>
@@ -21,14 +25,14 @@
 	<tests>
 		<test>
 			<!-- FASTQ-To-FASTA, keep N, don't rename -->
-			<param name="input" value="fastq_to_fasta1.fastq" />
+			<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
 			<param name="SKIPN" value=""/>
 			<param name="RENAMESEQ" value=""/>
 			<output name="output" file="fastq_to_fasta1a.out" />
 		</test>
 		<test>
 			<!-- FASTQ-To-FASTA, discard N, rename -->
-			<param name="input" value="fastq_to_fasta1.fastq" />
+			<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
 			<param name="SKIPN" value="no"/>
 			<param name="RENAMESEQ" value="yes"/>
 			<output name="output" file="fastq_to_fasta1b.out" />
diff --git a/tools/fastx_toolkit/fastx_artifacts_filter.xml b/tools/fastx_toolkit/fastx_artifacts_filter.xml
index 4980f7622f4..0defc79f17c 100644
--- a/tools/fastx_toolkit/fastx_artifacts_filter.xml
+++ b/tools/fastx_toolkit/fastx_artifacts_filter.xml
@@ -1,10 +1,14 @@
 <tool id="cshl_fastx_artifacts_filter" name="Remove sequencing artifacts">
 	<description></description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
-	<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"</command>
+	<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 
 	<inputs>
-		<param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to filter" />
+		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
 
 	</inputs>
 
diff --git a/tools/fastx_toolkit/fastx_barcode_splitter.xml b/tools/fastx_toolkit/fastx_barcode_splitter.xml
index 4b6fb9d2bfd..da3cd932cd1 100644
--- a/tools/fastx_toolkit/fastx_barcode_splitter.xml
+++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml
@@ -5,7 +5,7 @@
 
 	<inputs>
 		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
-		<param format="fasta,fastqsolexa" name="input" type="data" label="Library to split" />
+		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
 
 		<param name="EOL" type="select" label="Barcodes found at">
 			<option value="--bol">Start of sequence (5' end)</option>
@@ -22,7 +22,7 @@
 		<test>
 			<!-- Split a FASTQ file -->
 			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
-			<param name="input" value="fastx_barcode_splitter1.fastq" />
+			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
 			<param name="EOL" value="Start of sequence (5' end)" />
 			<param name="mismatches" value="2" />
 			<param name="partial" value="0" />
diff --git a/tools/fastx_toolkit/fastx_clipper.xml b/tools/fastx_toolkit/fastx_clipper.xml
index 4820d26612d..43be054dc6a 100644
--- a/tools/fastx_toolkit/fastx_clipper.xml
+++ b/tools/fastx_toolkit/fastx_clipper.xml
@@ -9,7 +9,7 @@
   </command>
   
   <inputs>
-    <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
+    <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" />
   
     <param name="minlength" size="4" type="integer" value="15">
       <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
@@ -56,7 +56,7 @@
 	#functional test with param value starting with - fails.	
 	<tests>
 		<test>
-			<param name="input" value="fastx_clipper1.fastq" />
+			<param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
 			<param name="maxmismatches" value="2" />
 			<param name="minlength" value="15" />
 			<param name="clip_source_list" value="user" />
diff --git a/tools/fastx_toolkit/fastx_collapser.xml b/tools/fastx_toolkit/fastx_collapser.xml
index cc4029ffd36..f8fe06c81ce 100644
--- a/tools/fastx_toolkit/fastx_collapser.xml
+++ b/tools/fastx_toolkit/fastx_collapser.xml
@@ -1,10 +1,14 @@
 <tool id="cshl_fastx_collapser" name="Collapse">
 	<description>sequences</description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
-	<command>zcat -f '$input' | fastx_collapser -v -o '$output' </command>
+	<command>zcat -f '$input' | fastx_collapser -v -o '$output' 
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 
 	<inputs>
-		<param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" />
+		<param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
 	</inputs>
 
     <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines. 
diff --git a/tools/fastx_toolkit/fastx_renamer.xml b/tools/fastx_toolkit/fastx_renamer.xml
index 258ec2541bb..db6bfd212c9 100644
--- a/tools/fastx_toolkit/fastx_renamer.xml
+++ b/tools/fastx_toolkit/fastx_renamer.xml
@@ -1,7 +1,11 @@
 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
 	<description></description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
-	<command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v </command>
+	<command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v 
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 
 	<inputs>
 		<param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
diff --git a/tools/fastx_toolkit/fastx_reverse_complement.xml b/tools/fastx_toolkit/fastx_reverse_complement.xml
index 66bb54f38ce..06e188ed575 100644
--- a/tools/fastx_toolkit/fastx_reverse_complement.xml
+++ b/tools/fastx_toolkit/fastx_reverse_complement.xml
@@ -1,9 +1,13 @@
 <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
 	<description></description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
-	<command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command>
+	<command>zcat -f '$input' | fastx_reverse_complement -v -o $output
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 	<inputs>
-		<param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
+		<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
 	</inputs>
 
 	<tests>
@@ -14,7 +18,7 @@
 		</test>
 		<test>
 			<!-- Reverse-complement a FASTQ file -->
-			<param name="input" value="fastx_rev_comp2.fastq" />
+			<param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
 			<output name="output" file="fastx_reverse_complement2.out" />
 		</test>
 	</tests>
diff --git a/tools/fastx_toolkit/fastx_trimmer.xml b/tools/fastx_toolkit/fastx_trimmer.xml
index f559121320a..3baa934571a 100644
--- a/tools/fastx_toolkit/fastx_trimmer.xml
+++ b/tools/fastx_toolkit/fastx_trimmer.xml
@@ -1,10 +1,14 @@
 <tool id="cshl_fastx_trimmer" name="Trim sequences">
 	<description></description>
 	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
-	<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output</command>
+	<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
 
 	<inputs>
-		<param format="fasta,fastqsanger" name="input" type="data" label="Library to clip" />
+		<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
 
 		<param name="first" size="4" type="integer" value="1">
 			<label>First base to keep</label>
@@ -25,7 +29,7 @@
 		</test>
 		<test>
 			<!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
-			<param name="input" value="fastx_trimmer2.fastq" />
+			<param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
 			<param name="first" value="1"/>
 			<param name="last" value="27"/>
 			<output name="output" file="fastx_trimmer2.out" />