--- a/make.fastq.xml	Tue Sep 05 16:08:25 2017 -0400
+++ b/make.fastq.xml	Wed Feb 14 09:12:55 2018 -0500
@@ -7,22 +7,22 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$qfile" qfile.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$qfile' qfile.dat &&
 
-        echo 'make.fastq(
-            fasta=fasta.dat,
-            qfile=qfile.dat
-            #if $chooseformat.use == "yes":
-                ,format=${chooseformat.format}
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'make.fastq(
+    fasta=fasta.dat,
+    qfile=qfile.dat
+    #if $chooseformat.use == "yes":
+        ,format=${chooseformat.format}
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
@@ -59,7 +59,12 @@
         <test><!-- test defaults -->
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
             <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
-            <output name="fastq" md5="e77b78321620e300946c23147ad599fd" ftype="fastqsanger"/>
+            <output name="fastq" ftype="fastqsanger">
+                <assert_contents>
+                    <expand macro="test-fastq-format"/>
+                    <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
+                </assert_contents>
+            </output>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with quality score format conversion -->
@@ -67,22 +72,26 @@
             <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
             <param name="use" value="yes"/>
             <param name="format" value="illumina"/>
-            <output name="fastq" md5="c792253da205d4d1c66bc87a2969aa25" ftype="fastqillumina"/>
+            <output name="fastq" ftype="fastqillumina">
+                <assert_contents>
+                    <expand macro="test-fastq-format"/>
+                    <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
+                </assert_contents>
+            </output>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-        <![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The fastq.info_ command reads a fasta file and quality file and creates a fastq.
+The make.fastq_ command reads a fasta file and quality file and creates a fastq.
 
 
-.. _fastq.info: https://www.mothur.org/wiki/Make.fastq
-]]>
-    </help>
+.. _make.fastq: https://www.mothur.org/wiki/Make.fastq
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>