annotate test-data/meme_output_test2.xml @ 16:3c2ac7c3f0b8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"

<?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" >
<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 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 sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
</MEME>