--- a/dexseq_count.xml	Sat Jul 28 03:44:02 2018 -0400
+++ b/dexseq_count.xml	Tue Dec 11 00:19:18 2018 -0500
@@ -4,7 +4,6 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="0.9.1">htseq</requirement>
     </expand>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -22,11 +21,11 @@
         '$flattened_gtf_out'
 #elif $mode.mode_select == "count":
     dexseq_count.py
-        -f bam
-        -p $mode.paired
-        -s $mode.stranded
-        -a $mode.qual
-        -r $mode.order
+        --format bam
+        --paired $mode.paired
+        --stranded $mode.stranded
+        --minaqual $mode.qual
+        --order $mode.order
         $mode.flattened_gtf_in
         '$mode.bamfile'
         '$counts_file'
@@ -47,15 +46,15 @@
             <when value="count">
                 <param name="bamfile" type="data" format="bam" label="Input bam file"/>
                 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
-                <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/>
+                <param name="paired" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Is library paired end?"/>
                 <param name="stranded" type="select" label="Is library strand specific?">
+                    <option value="yes" selected="true">Yes</option>
                     <option value="no">No</option>
-                    <option value="yes">Yes</option>
                     <option value="reverse">Yes, but reverse</option>
                 </param>
                 <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/>
                 <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data">
-                    <option value="pos">By position</option>
+                    <option value="pos" selected="true">By position</option>
                     <option value="name">By name</option>
                 </param>
             </when>
@@ -63,10 +62,10 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
+        <data name="counts_file" format="tabular" label="DEXSeq count reads on ${on_string}">
             <filter>mode['mode_select'] == 'count'</filter>
         </data>
-        <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}">
+        <data name="flattened_gtf_out" format="gtf" label="DEXSeq prepare annotation on ${on_string}">
             <filter>mode['mode_select'] == 'prepare'</filter>
         </data>
     </outputs>
@@ -83,6 +82,7 @@
             <param name="mode_select" value="count" />
             <param name="bamfile" ftype="bam" value="in.bam" />
             <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>
+            <param name="stranded" value="no" />
             <output name="counts_file" ftype="tabular" file="out_count.tab"/>
         </test>
     </tests>
@@ -97,12 +97,12 @@
 
 **Inputs**
 
-Mode-preprare: Takes a normal gtf file as input. For example from Ensembl database.
+Mode-preprare: Takes a normal GTF file as input. For example from Ensembl database.
 Mode-count: Inputs are flattened GTF file and BAM file. The flattened GTF file can be generated from 'prepare' mode of this tool.
 
 **Output**
 
-Mode-prepare: Flattened GTF file that contains only exons with corresponding gene ids from given GTF file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used.
+Mode-prepare: Flattened GTF file that contains only exons with corresponding gene ids from the input GTF file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used.
 Mode-count: Two column tab-delimited file with exon ids and their read counts.
 
 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html