--- a/test-data/fimo_output_xml_2.xml	Thu Jun 16 08:07:03 2016 -0400
+++ b/test-data/fimo_output_xml_2.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -4,14 +4,9 @@
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
 >
-<command-line>fimo --alpha 1.000000 --max-stored-scores 100000 --motif-pseudo 0.100000 --no-qvalue --thresh 0.000100 --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
 <settings>
-<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files</setting>
-<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
-<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
 <setting name="allow clobber">false</setting>
 <setting name="compute q-values">false</setting>
-<setting name="parse genomic coord.">false</setting>
 <setting name="text only">false</setting>
 <setting name="scan both strands">false</setting>
 <setting name="output threshold">0.0001</setting>