--- a/test-data/meme_output_test2.xml	Sat Nov 27 14:38:35 2021 +0000
+++ b/test-data/meme_output_test2.xml	Sat Apr 09 08:34:02 2022 +0000
@@ -1,82 +1,58 @@
-<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
-<!-- Document definition -->
-<!DOCTYPE MEME[
-<!ELEMENT MEME (
-  training_set,
-  model, 
-  motifs, 
-  scanned_sites_summary?
-)>
-<!ATTLIST MEME 
-  version CDATA #REQUIRED
-  release CDATA #REQUIRED
-<!-- Training-set elements -->
-<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>
-<!ATTLIST training_set primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED
-  control_sequences CDATA "" control_count CDATA "" control_positions CDATA "">
-<!ELEMENT alphabet (letter*)>
-<!ATTLIST alphabet name CDATA #REQUIRED>
-<!ELEMENT letter_frequencies (alphabet_array)>
-<!-- Model elements -->
-<!ELEMENT model (
-  command_line,
-  host,
-  type,
-  nmotifs,
-)>
-<!ELEMENT command_line (#PCDATA)*>
-<!ELEMENT motifs (motif*)>
-<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
-<!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
-<!ELEMENT left_flank (#PCDATA)>
-<!-- The site contains the sequence for the motif instance -->
-<!ELEMENT site (letter_ref*)>
-<!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
-<!ELEMENT right_flank (#PCDATA)>
-<!-- Scanned site elements -->
-<!-- Scanned sites are motif occurences found during the sequence scan phase -->
-<!ELEMENT scanned_sites_summary (scanned_sites*)>
-<training_set primary_sequences="Galaxy_FASTA_Input" primary_count="30" primary_positions="1500" control_sequences="--none--" control_count="0" control_positions="0">
-<alphabet name="DNA" like="dna">
-<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
-<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
-<value letter_id="G">0.257</value>
-<value letter_id="T">0.217</value>
-</alphabet_array>
-<model>
-<type>zoops</type>
-<scores>
-<alphabet_matrix>
-<alphabet_array>
-<value letter_id="A">-14</value>
-<value letter_id="A">3</value>
-<value letter_id="A">-1155</value>
-<value letter_id="A">156</value>
-<value letter_id="A">-1155</value>
-<value letter_id="A">172</value>
-<value letter_id="A">125</value>
-<value letter_id="A">167</value>
-<value letter_id="A">144</value>
-<value letter_id="A">0.266667</value>
-<value letter_id="A">0.300000</value>
-<value letter_id="A">0.800000</value>
-<contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >
-<left_flank>AAGGCCAGGA</left_flank>
-<letter_ref letter_id="G"/>
-<right_flank>GCCTGAGAGC</right_flank>
-<contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >
-<letter_ref letter_id="A"/>
-<contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
-<right_flank>AGCCCTGTAC</right_flank>
-<contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
-<left_flank>CGTGGTCGCG</left_flank>
-<right_flank>GC</right_flank>
-<contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >
-<left_flank>GCTGCCGGTG</left_flank>
-<right_flank>GCCCTGGCG</right_flank>
-<contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >
+</motifs>
 <scanned_sites_summary p_thresh="0.0001">
 <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>
+</scanned_sites>
 <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/>
+</scanned_sites>
 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>
+</scanned_sites>
+</scanned_sites_summary>
 </MEME>