annotate test-data/streme_output_test3.xml @ 20:faa378fa0c81 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278

      <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>
    <strands>none</strands>
    <sequence_db A="0.275" C="0.224" D="0" E="0" F="0" G="0.283" H="0" I="0" K="0" L="0" M="0.00977" N="0" P="0" Q="0" R="0" S="0" T="0.209" V="0" W="0" Y="0"/>
    <background_frequencies source="--negatives--" order="0">
      <alphabet_array>
        <value letter_id="A">0.279</value>
        <value letter_id="C">0.225</value>
        <value letter_id="D">3.03e-05</value>
        <value letter_id="E">3.03e-05</value>
        <value letter_id="F">3.03e-05</value>
        <value letter_id="G">0.28</value>
        <value letter_id="H">3.03e-05</value>
        <value letter_id="I">3.03e-05</value>
        <value letter_id="K">3.03e-05</value>
        <value letter_id="L">3.03e-05</value>
        <value letter_id="M">0.0079</value>
        <value letter_id="N">3.03e-05</value>
        <value letter_id="P">3.03e-05</value>
        <value letter_id="Q">3.03e-05</value>
        <value letter_id="R">3.03e-05</value>
        <value letter_id="S">3.03e-05</value>
        <value letter_id="T">0.208</value>
        <value letter_id="V">3.03e-05</value>
        <value letter_id="W">3.03e-05</value>
        <value letter_id="Y">3.03e-05</value>
      </alphabet_array>
    </background_frequencies>
    <stop nmotifs="5"/>
    <objfun>Differential Enrichment</objfun>
    <test>Fisher Exact Test</test>
    <minw>5</minw>
    <maxw>20</maxw>
    <kmer>1</kmer>
    <hofract>0.1</hofract>
    <neval>25</neval>
    <nref>4</nref>
    <niter>20</niter>
    <patience>3</patience>
    <seed>0</seed>
    <notrim>no</notrim>
    <useer>no</useer>
    <minscore>0</minscore>
    <ignore_depth>5</ignore_depth>
    <nsubsets>1</nsubsets>
    <min_pal_ratio>0.85</min_pal_ratio>
    <max_pal_ed>5</max_pal_ed>
    <cand>no</cand>
    <experimental>no</experimental>
    <totallength>0</totallength>