--- a/fimo.xml	Thu Apr 14 11:22:23 2016 -0400
+++ b/fimo.xml	Thu Jun 16 08:06:53 2016 -0400
@@ -33,8 +33,8 @@
                 --motif_pseudo "${options_type.motif_pseudo}"
                 ${options_type.no_qvalue}
                 ${options_type.norc}
-                ${options_type.parse_genomic_coord_cond.parse_genomic_coord}
-                #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == '--parse_genomic_coord':
+                #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
+                    --parse_genomic_coord 'yes'
                     --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
                 #end if
                 #if str($options_type.psp_cond.psp_selector) == 'yes':
@@ -112,14 +112,14 @@
                 <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/>
                 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
                 <conditional name="parse_genomic_coord_cond">
-                    <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" />
-                    <when value="--parse_genomic_coord">
-                        <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
-                            <option value="no" selected="true">No</option>
-                            <option value="yes">Yes</option>
-                        </param>
+                    <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="yes">
+                        <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" />
                     </when>
-                    <when value=""/>
+                    <when value="no"/>
                 </conditional>
                 <conditional name="psp_cond">
                     <param name="psp_selector" type="select" label="Use position-specific priors?">
@@ -232,7 +232,7 @@
             <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/>
             <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
             <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
-            <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/>
+            <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/>
             <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
         </test>
         <test>
@@ -244,7 +244,7 @@
             <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
             <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
             <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
-            <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/>
+            <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
             <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
         </test>
         <test>
@@ -259,9 +259,9 @@
             <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
             <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
             <output_collection name="motifs" type="list">
-                <element name="MOTIFS1.gff" file="fimo_output_almost-gff_2.txt" ftype="gff" compare="contains"/>
+                <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
             </output_collection>
-            <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/>
+            <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
             <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
         </test>
     </tests>