Mercurial > repos > iuc > meme_fimo

diff test-data/dreme_fimo_input_1.xml @ 13:4eb02864e5df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:00 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dreme_fimo_input_1.xml	Thu May 17 14:11:00 2018 -0400
@@ -0,0 +1,99 @@
+<dreme version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
+  <model>
+    <command_line>dreme -oc dreme_out -norc -p input.fa</command_line>
+    <positives name="input" count="1000" file="input.fa" last_mod_date="Wed May 02 16:37:00 CEST 2018" />
+    <negatives name="shuffled positive sequences" count="1000" from="shuffled"/>
+    <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>
+    <strands>given</strands>
+    <background A="0.294" C="0.209" G="0.164" T="0.333" from="dataset"/>
+    <stop evalue="0.05"/>
+    <ngen>100</ngen>
+    <add_pv_thresh>0.01</add_pv_thresh>
+    <seed>1</seed>
+    <host>ThinkPad-T450s</host>
+    <when>Wed May 02 16:45:34 CEST 2018</when>
+  </model>
+  <motifs>
+    <motif id="m01" alt="DREME-1" seq="ACTAAYH" length="7" nsites="405" p="371" n="75" pvalue="9.7e-061" evalue="4.9e-056" unerased_evalue="4.9e-056">
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.600000" G="0.000000" T="0.400000"/>
+      <pos A="0.471605" C="0.244444" G="0.000000" T="0.283951"/>
+      <match seq="ACTAACA" p="108" n="10" pvalue="2.6e-023" evalue="1.3e-018"/>
+      <match seq="ACTAACC" p="62" n="7" pvalue="9.5e-013" evalue="4.8e-008"/>
+      <match seq="ACTAATA" p="77" n="18" pvalue="1.5e-010" evalue="7.4e-006"/>
+      <match seq="ACTAACT" p="62" n="16" pvalue="4.4e-008" evalue="2.2e-003"/>
+      <match seq="ACTAATC" p="35" n="8" pvalue="1.7e-005" evalue="8.8e-001"/>
+      <match seq="ACTAATT" p="48" n="20" pvalue="3.7e-004" evalue="1.9e+001"/>
+    </motif>
+    <motif id="m02" alt="DREME-2" seq="YTAACA" length="6" nsites="197" p="170" n="59" pvalue="1.8e-015" evalue="9.0e-011" unerased_evalue="6.8e-031">
+      <pos A="0.000000" C="0.365482" G="0.000000" T="0.634518"/>
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <match seq="TTAACA" p="118" n="38" pvalue="8.6e-012" evalue="4.3e-007"/>
+      <match seq="CTAACA" p="63" n="21" pvalue="1.6e-006" evalue="7.8e-002"/>
+    </motif>
+    <motif id="m03" alt="DREME-3" seq="TCTGT" length="5" nsites="220" p="208" n="101" pvalue="1.9e-011" evalue="9.2e-007" unerased_evalue="4.4e-007">
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <match seq="TCTGT" p="208" n="101" pvalue="1.9e-011" evalue="9.2e-007"/>
+    </motif>
+    <motif id="m04" alt="DREME-4" seq="SCCAGG" length="6" nsites="58" p="58" n="14" pvalue="5.0e-008" evalue="2.4e-003" unerased_evalue="1.5e-003">
+      <pos A="0.000000" C="0.620690" G="0.379310" T="0.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
+      <match seq="CCCAGG" p="36" n="9" pvalue="2.7e-005" evalue="1.3e+000"/>
+      <match seq="GCCAGG" p="22" n="5" pvalue="7.1e-004" evalue="3.4e+001"/>
+    </motif>
+    <motif id="m05" alt="DREME-5" seq="CCAGCAY" length="7" nsites="27" p="27" n="1" pvalue="9.2e-008" evalue="4.4e-003" unerased_evalue="2.3e-003">
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
+      <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.518519" G="0.000000" T="0.481481"/>
+      <match seq="CCAGCAC" p="14" n="0" pvalue="5.8e-005" evalue="2.8e+000"/>
+      <match seq="CCAGCAT" p="13" n="1" pvalue="8.9e-004" evalue="4.3e+001"/>
+    </motif>
+    <motif id="m06" alt="DREME-6" seq="GMATGT" length="6" nsites="60" p="59" n="18" pvalue="9.9e-007" evalue="4.8e-002" unerased_evalue="4.8e-002">
+      <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
+      <pos A="0.533333" C="0.466667" G="0.000000" T="0.000000"/>
+      <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
+      <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
+      <match seq="GCATGT" p="28" n="8" pvalue="5.4e-004" evalue="2.6e+001"/>
+      <match seq="GAATGT" p="32" n="11" pvalue="8.6e-004" evalue="4.1e+001"/>
+    </motif>
+  </motifs>
+  <run_time cpu="30.86" real="30.97" stop="evalue"/>
+</dreme>