--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_xml_1.xml	Tue Dec 22 17:01:51 2015 -0500
@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Begin document body -->
+<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
+>
+<command-line>fimo --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_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/001/1973/dataset_2713_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">true</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>
+<setting name="threshold type">p-value</setting>
+<setting name="max stored scores">100000</setting>
+<setting name="pseudocount">0.1</setting>
+<setting name="verbosity">1</setting>
+</settings>
+<sequence-data num-sequences="1" num-residues="5386" />
+<alphabet name="Protein" like="protein">
+<letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
+<letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
+<letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
+<letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
+<letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
+<letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
+<letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
+<letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
+<letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
+<letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
+<letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
+<letter id="N" symbol="N" name="Asparagine" colour="008000"/>
+<letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
+<letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
+<letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
+<letter id="S" symbol="S" name="Serine" colour="008000"/>
+<letter id="T" symbol="T" name="Threonine" colour="008000"/>
+<letter id="V" symbol="V" name="Valine" colour="0000CC"/>
+<letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
+<letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
+<letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
+<letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
+<letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
+<letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
+</alphabet>
+<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
+<background source="non-redundant database">
+<value letter="A">0.073</value>
+<value letter="C">0.018</value>
+<value letter="D">0.052</value>
+<value letter="E">0.062</value>
+<value letter="F">0.040</value>
+<value letter="G">0.069</value>
+<value letter="H">0.022</value>
+<value letter="I">0.056</value>
+<value letter="K">0.058</value>
+<value letter="L">0.092</value>
+<value letter="M">0.023</value>
+<value letter="N">0.046</value>
+<value letter="P">0.051</value>
+<value letter="Q">0.041</value>
+<value letter="R">0.052</value>
+<value letter="S">0.074</value>
+<value letter="T">0.059</value>
+<value letter="V">0.064</value>
+<value letter="W">0.013</value>
+<value letter="Y">0.033</value>
+</background>
+<cisml-file>cisml.xml</cisml-file>
+</fimo>