Mercurial > repos > iuc > meme_meme
diff 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
author | iuc |
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date | Thu, 17 May 2018 14:10:48 -0400 |
parents | |
children | 3f0dd362b755 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test3.xml Thu May 17 14:10:48 2018 -0400 @@ -0,0 +1,56 @@ +<?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>