Mercurial > repos > iuc > meme_meme

diff test-data/meme_output_test1.xml @ 20:faa378fa0c81 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
author iuc
date Mon, 14 Jul 2025 21:33:26 +0000
parents 19237efe98d1
children
line wrap: on
line diff
--- a/test-data/meme_output_test1.xml	Thu Aug 29 10:20:10 2024 +0000
+++ b/test-data/meme_output_test1.xml	Mon Jul 14 21:33:26 2025 +0000
@@ -1,3 +1,924 @@
+<alphabet_array>
+<value letter_id="A">-32</value>
+<value letter_id="C">-680</value>
+<value letter_id="D">91</value>
+<value letter_id="E">77</value>
+<value letter_id="F">7</value>
+<value letter_id="G">138</value>
+<value letter_id="H">-20</value>
+<value letter_id="I">55</value>
+<value letter_id="K">64</value>
+<value letter_id="L">107</value>
+<value letter_id="M">11</value>
+<value letter_id="N">150</value>
+<value letter_id="P">142</value>
+<value letter_id="Q">72</value>
+<value letter_id="R">87</value>
+<value letter_id="S">396</value>
+<value letter_id="T">-148</value>
+<value letter_id="V">221</value>
+<value letter_id="W">-140</value>
+<value letter_id="Y">-36</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">-11</value>
+<value letter_id="C">-680</value>
+<value letter_id="D">89</value>
+<value letter_id="E">76</value>
+<value letter_id="F">7</value>
+<value letter_id="G">137</value>
+<value letter_id="H">-21</value>
+<value letter_id="I">55</value>
+<value letter_id="K">63</value>
+<value letter_id="L">107</value>
+<value letter_id="M">10</value>
+<value letter_id="N">149</value>
+<value letter_id="P">141</value>
+<value letter_id="Q">71</value>
+<value letter_id="R">87</value>
+<value letter_id="S">396</value>
+<value letter_id="T">-239</value>
+<value letter_id="V">220</value>
+<value letter_id="W">-140</value>
+<value letter_id="Y">-36</value>
+</alphabet_array>
+<alphabet_array>
+<value letter_id="A">-79</value>
+<value letter_id="C">41</value>
+<value letter_id="D">4</value>
+<value letter_id="E">21</value>
+<value letter_id="F">-7</value>
+<value letter_id="G">44</value>
+<value letter_id="H">-62</value>
+<value letter_id="I">42</value>
+<value letter_id="K">-5</value>
+<value letter_id="L">99</value>
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+<value letter_id="S">399</value>
+<value letter_id="T">-46</value>
+<value letter_id="V">223</value>
+<value letter_id="W">-173</value>
+<value letter_id="Y">-68</value>
+</alphabet_array>
+<alphabet_array>
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+<value letter_id="F">-2</value>
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+<value letter_id="H">-43</value>
+<value letter_id="I">46</value>
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+<value letter_id="M">3</value>
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+<value letter_id="Q">60</value>
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+<value letter_id="S">397</value>
+<value letter_id="T">-235</value>
+<value letter_id="V">220</value>
+<value letter_id="W">-160</value>
+<value letter_id="Y">-55</value>
+</alphabet_array>
+<alphabet_array>
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+<value letter_id="C">-820</value>
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+<value letter_id="T">212</value>
+<value letter_id="V">127</value>
+<value letter_id="W">-193</value>
+<value letter_id="Y">-95</value>
+</alphabet_array>
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+<value letter_id="D">70</value>
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+<value letter_id="F">77</value>
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+<value letter_id="M">90</value>
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+<value letter_id="P">124</value>
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+<value letter_id="R">107</value>
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+</alphabet_array>
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+</alphabet_array>
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+<value letter_id="V">52</value>
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+<value letter_id="Y">-153</value>
+</alphabet_array>
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+</alphabet_array>
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+<left_flank>ACAGGCCCTG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<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>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCCCAGCAG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_9" position="13" strand="none" pvalue="3.41e-06" >
+<left_flank>GATTCACTGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GGCCCTCTGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_21" position="7" strand="none" pvalue="4.00e-06" >
+<left_flank>CCAAGGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCCCACAAA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_13" position="13" strand="none" pvalue="5.01e-06" >
+<left_flank>CCACCAGCTT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>AGCCCTGTAC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_23" position="15" strand="none" pvalue="6.06e-06" >
+<left_flank>ATACCCAGGG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>CCTCAGCAGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_15" position="21" strand="none" pvalue="8.67e-06" >
+<left_flank>AATCACTGAG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GTCCCAGGGA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_12" position="18" strand="none" pvalue="8.67e-06" >
+<left_flank>CACCAGAGCT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>AGAAGGTTCT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_11" position="16" strand="none" pvalue="8.67e-06" >
+<left_flank>CACTATTGAA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TTTCATTTGC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_22" position="2" strand="none" pvalue="1.21e-05" >
+<left_flank>GA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCCAACATCC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_28" position="32" strand="none" pvalue="1.59e-05" >
+<left_flank>CCGGCGGGGC</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GGGGCGG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_20" position="4" strand="none" pvalue="1.59e-05" >
+<left_flank>CAGA</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GTTCCGACCA</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_6" position="15" strand="none" pvalue="1.68e-05" >
+<left_flank>CCCACTACTT</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TCATTCTGAG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_14" position="19" strand="none" pvalue="2.03e-05" >
+<left_flank>CACCAGCAAG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GCTCAGGAGT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_4" position="12" strand="none" pvalue="3.06e-05" >
+<left_flank>CAGGTCTAAG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>CTTGGAGTCC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_0" position="39" strand="none" pvalue="3.06e-05" >
+<left_flank>CCTCGGGACG</left_flank>
+<site>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank></right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_18" position="37" strand="none" pvalue="3.82e-05" >
+<left_flank>CGTGGTCGCG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_5" position="0" strand="none" pvalue="3.82e-05" >
+<left_flank></left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>ATGGTCCTGT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_29" position="30" strand="none" pvalue="4.02e-05" >
+<left_flank>GCTGCCGGTG</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+</site>
+<right_flank>GCCCTGGCG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_1" position="27" strand="none" pvalue="5.52e-05" >
+<left_flank>AGTCACAAGT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>GGGTCGCACG</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_3" position="14" strand="none" pvalue="5.94e-05" >
+<left_flank>CCCAGGTTTC</left_flank>
+<site>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TCGCCGCACC</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_16" position="22" strand="none" pvalue="6.78e-05" >
+<left_flank>AGTTTCAGTT</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="C"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>attatataac</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_7" position="2" strand="none" pvalue="2.08e-04" >
+<left_flank>TC</left_flank>
+<site>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+</site>
+<right_flank>AAATGTTCCT</right_flank>
+</contributing_site>
+<contributing_site sequence_id="sequence_8" position="13" strand="none" pvalue="4.05e-04" >
+<left_flank>TATAACTCAG</left_flank>
+<site>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="G"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="T"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+<letter_ref letter_id="A"/>
+</site>
+<right_flank>TAATTTGTAC</right_flank>
+</contributing_site>
+</contributing_sites>
+</motif>
 </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"/>