annotate test-data/fimo_output_test3.xml @ 13:57e5d9382f36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Begin document body -->
<fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<command-line>fimo -o ./fimo_test4_out --thresh 0.01 --bgfile --uniform-- --max-stored-scores 100000 --motif ACTAAYH --motif-pseudo 0.1 dreme_fimo_input_1.xml hsa_chrM.fa</command-line>
<settings>
<setting name="output directory">./fimo_test4_out</setting>
<setting name="MEME file name">dreme_fimo_input_1.xml</setting>
<setting name="sequence file name">hsa_chrM.fa</setting>
<setting name="background file name">--uniform--</setting>
<setting name="allow clobber">false</setting>
<setting name="compute q-values">true</setting>
<setting name="parse genomic coord.">false</setting>
<setting name="text only">false</setting>
<setting name="scan both strands">true</setting>
<setting name="output threshold">0.01</setting>
<setting name="threshold type">p-value</setting>
<setting name="max stored scores">100000</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">2</setting>
<setting name="selected motif">ACTAAYH</setting>
</settings>
<sequence-data num-sequences="1" num-residues="16569" />
<alphabet name="DNA" like="dna">
<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
<letter id="V" symbol="V" equals="ACG" name="Not T"/>
<letter id="H" symbol="H" equals="ACT" name="Not G"/>
<letter id="D" symbol="D" equals="AGT" name="Not C"/>
<letter id="B" symbol="B" equals="CGT" name="Not A"/>
<letter id="M" symbol="M" equals="AC" name="Amino"/>
<letter id="R" symbol="R" equals="AG" name="Purine"/>
<letter id="W" symbol="W" equals="AT" name="Weak"/>
<letter id="S" symbol="S" equals="CG" name="Strong"/>
<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
<letter id="K" symbol="K" equals="GT" name="Keto"/>
</alphabet>
<motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/>
<motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
<motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
<motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
<motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
<background source="--uniform--">
<value letter="A">0.250</value>
<value letter="C">0.250</value>
<value letter="G">0.250</value>
<value letter="T">0.250</value>
</background>
<cisml-file>cisml.xml</cisml-file>
</fimo>