comparison test-data/fimo_output_test2.xml @ 15:0c5239d1aa65 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"

14:c1a9a297ba8b

<?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 -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa</command-line>
<settings>
<setting name="output directory">fimo_test2_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">fimo_background_probs_hsa_chrM.txt</setting>
<setting name="allow clobber">true</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">0.0001</setting>

<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="fimo_background_probs_hsa_chrM.txt">
<value letter="A">0.278</value>
<value letter="C">0.222</value>
<value letter="G">0.222</value>
<value letter="T">0.278</value>
</background>

15:0c5239d1aa65

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Begin document body -->
<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<settings>
<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">0.0001</setting>

<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"/>
<value letter="A">0.278</value>
<value letter="C">0.222</value>
<value letter="G">0.222</value>
<value letter="T">0.278</value>
</background>