diff test-data/meme_output_test1.xml @ 5:f33d77dcacce draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"

--- a/test-data/meme_output_test1.xml	Sat Nov 27 14:39:01 2021 +0000
+++ b/test-data/meme_output_test1.xml	Sat Apr 09 08:32:58 2022 +0000
@@ -1,118 +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)>
-                   name CDATA #REQUIRED
-                   length CDATA #REQUIRED
-                   weight CDATA #REQUIRED
-<!ELEMENT letter_frequencies (alphabet_array)>
-<!-- Model elements -->
-<!ELEMENT model (
-  command_line,
-  host,
-  type,
-  nmotifs,
-)>
-<!ELEMENT command_line (#PCDATA)*>
-<!ELEMENT host (#PCDATA)*>
-<!ELEMENT type (#PCDATA)*>
-<!ELEMENT nmotifs (#PCDATA)*>
-<!-- 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*)>
-<!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
-<!ELEMENT scanned_sites (scanned_site*)>
-<!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
-                        pvalue CDATA #REQUIRED
-                        num_sites CDATA #REQUIRED>
-<!ELEMENT scanned_site EMPTY>
-<!ATTLIST scanned_site  motif_id IDREF #REQUIRED
-                        strand (plus|minus|none) 'none'
-                        position CDATA #REQUIRED
-                        pvalue CDATA #REQUIRED>
-<!-- Utility elements -->
-<!-- A reference to a letter in the alphabet -->
-<!ELEMENT letter_ref EMPTY>
-<!ATTLIST letter_ref letter_id IDREF #REQUIRED>
-<!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
-<!ELEMENT alphabet_array (value*)>
-<!ELEMENT value (#PCDATA)>
-<!ATTLIST value letter_id IDREF #REQUIRED>
-<!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
-<!ELEMENT alphabet_matrix (alphabet_array*)>
-]>
-<!-- Begin document body -->
-<MEME version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
-<alphabet name="Protein" like="protein">
-<letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
-</alphabet>
-<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
-<letter_frequencies>
-<alphabet_array>
-<value letter_id="A">0.294</value>
-</letter_frequencies>
-</training_set>
-<model>
-<scores>
-<alphabet_matrix>
-<value letter_id="A">-32</value>
-<value letter_id="A">-79</value>
-<value letter_id="A">11</value>
-<value letter_id="A">-596</value>
-<value letter_id="A">165</value>
-<value letter_id="A">-838</value>
-<value letter_id="A">176</value>
-<value letter_id="A">134</value>
-<value letter_id="A">165</value>
-<value letter_id="A">147</value>
-<value letter_id="A">0.240000</value>
-<value letter_id="A">0.280000</value>
-<value letter_id="A">0.160000</value>
-<value letter_id="A">0.320000</value>
-<value letter_id="A">0.000000</value>
-<value letter_id="A">0.960000</value>
-<value letter_id="A">0.000000</value>
-<value letter_id="A">1.000000</value>
-<value letter_id="A">0.760000</value>
-<value letter_id="A">0.960000</value>
-<value letter_id="A">0.840000</value>
-</alphabet_matrix>
-</probabilities>
-<regular_expression>
-[GA][GA][GC][GA]TATA[AT]AA
-</regular_expression>
-<contributing_sites>
-<contributing_site sequence_id="sequence_24" position="12" strand="none" pvalue="1.06e-06" >
-<left_flank>AAGGCCAGGA</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-</site>
-<right_flank>GCCTGAGAGC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_25" position="36" strand="none" pvalue="3.41e-06" >
-<left_flank>ACAGGCCCTG</left_flank>
-<right_flank>GCC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_19" position="9" strand="none" pvalue="3.41e-06" >
-<left_flank>CAGGCCCTG</left_flank>
-<right_flank>GCCCCAGCAG</right_flank>
+</motifs>
+<scanned_sites_summary p_thresh="0.0001">
+<scanned_sites sequence_id="sequence_0" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="39" pvalue="3.06e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_1" pvalue="2.21e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="27" pvalue="5.52e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_2" pvalue="7.29e-01" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_3" pvalue="2.37e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="14" pvalue="5.94e-05"/>
+</scanned_sites>
 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="3.06e-05"/>
+</scanned_sites>
 <scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/>
+</scanned_sites>
 <scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites>
+<scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/>
+</scanned_sites>
+<scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/>
+</scanned_sites>
+</scanned_sites_summary>
 </MEME>