Mercurial > repos > iuc > meme_chip

annotate meme_chip.xml @ 0:6095db402811 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
author iuc
date Fri, 20 Apr 2018 09:03:44 -0400
parents
children 091a9d638d78
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0
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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1 <tool id="meme_chip" name="MEME-ChIP" version="4.11.2">
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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3 <macros>
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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4 <import>macros.xml</import>
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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5 </macros>
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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6 <expand macro="requirements" />
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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7 <code file="get_meme_motif_databases.py" />
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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8 <command detect_errors="exit_code"><![CDATA[
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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9 #import os
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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10 #set primary_output = $os.path.join($output.files_path, "index.html")
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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11 meme-chip '$input'
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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12 -noecho
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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13 #if $control:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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14 -neg '$control'
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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15 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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16 $sequence_alphabet
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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17 -o '$output.files_path'
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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18 #if str($options_type_cond.options_type)=='advanced':
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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19 ## FIXME: CentriMo cannot be run, See the comments in the input section.
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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21 ## #if str($run_centrimo) == "yes":
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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23 ## #if $options_type_cond.run_centrimo_cond.centrimo_local:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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24 ## -centrimo-local
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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25 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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26 ## #if $options_type_cond.run_centrimo_cond.centrimo_score:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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28 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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29 ## #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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31 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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32 ## #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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34 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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35 ## #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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36 ## -centrimo-noseq
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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37 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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38 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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39 ## -centrimo-flip
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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40 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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41 ## #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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42 $options_type_cond.search_given_strand
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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43 -order $options_type_cond.background_model_order
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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44 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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45 -norand
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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46 #if $options_type_cond.subsampling_cond.subsampling.seed:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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47 -seed $options_type_cond.subsampling_cond.subsampling.seed
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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48 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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49 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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50 #if $options_type_cond.nmeme:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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51 -nmeme $options_type_cond.nmeme
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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52 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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53 #if $options_type_cond.ccut:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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54 -ccut $options_type_cond.ccut
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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55 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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56 -group-thresh $options_type_cond.group_threash
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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57 #if str($options_type_cond.group_weak):
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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58 -group-weak $options_type_cond.group_weak
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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59 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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60 -filter-thresh $options_type_cond.filter_thresh
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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61 $options_type_cond.old_clustering
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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62 -meme-mod $options_type_cond.meme_mod
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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63 #if $options_type_cond.meme_minw:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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64 -meme-minw $options_type_cond.meme_minw
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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65 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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66 #if $options_type_cond.meme_maxw:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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67 -meme-maxw $options_type_cond.meme_maxw
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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68 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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69 #if $options_type_cond.meme_nmotifs:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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70 -meme-nmotifs $options_type_cond.meme_nmotifs
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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71 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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72 #if $options_type_cond.meme_minsites:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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73 -meme-minsites $options_type_cond.meme_minsites
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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74 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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75 #if $options_type_cond.meme_maxsites:
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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76 -meme-maxsites $options_type_cond.meme_maxsites
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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77 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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78 $options_type_cond.meme_pal
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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79 -dreme-e $options_type_cond.dreme_e
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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80 -dreme-m $options_type_cond.dreme_m
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
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81 -spamo-skip
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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82 -fimo-skip
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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83 #end if
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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84 && rm '$output'
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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85 && ln -s $primary_output '$output'
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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86 ]]></command>
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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87 <inputs>
6095db402811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
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88 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
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89 <param name="control" type="data" format="fasta" optional="true" label="Control sequences" help="If no selection, positive sequences in the input are shuffled to create the negative set"/>
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90 <param name="sequence_alphabet" type="select" label="Sequence alphabet">
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91 <option value="-dna" selected="true">DNA</option>
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92 <option value="-rna">RNA</option>
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93 </param>
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94 <conditional name="options_type_cond">
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95 <param name="options_type" type="select" label="Options Configuration">
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96 <option value="basic" selected="true">Basic</option>
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97 <option value="advanced">Advanced</option>
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98 </param>
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99 <when value="basic"/>
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100 <when value="advanced">
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101 <!--
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102 FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below.
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103 <conditional name="run_centrimo_cond">
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104 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?">
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105 <option value="yes" selected="true">Yes</option>
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106 <option value="no">No</option>
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107 </param>
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108 <when value="yes">
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109
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110 We have 2 dynamic select lists here. The first select list (meme_motif_database_dir) is populated from the meme_motif_databases
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111 data table. The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir
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112 select list is changed. This composition used to work (see Examples->Dynamic Options section of
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113 https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does. We'll have to figure out what is broken in
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114 the dynamic options code in ~/parameters/basic.py in order to uncomment this block.
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115
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116 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True">
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117 <options from_data_table="meme_motif_databases">
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118 <filter type="sort_by" column="1"/>
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119 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
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120 </options>
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121 </param>
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122 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/>
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123 <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/>
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124 <param name="centrimo_score" type="integer" optional="true" value="0" min="0" label="Minimum allowed CentriMo match score"/>
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125 <param name="centrimo_maxreg" type="integer" optional="true" value="0" min="0" label="Maximum CentriMo region size to be considered"/>
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126 <param name="centrimo_ethresh" type="integer" optional="true" value="0" min="0" label="CentriMo E-value threshold for reporting" />
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127 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
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128 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
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129 </when>
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130 <when value="no"/>
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131 </conditional>
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132 -->
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133 <param name="background_model_order" type="select" label="Select the order of the Markov background model">
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134 <option value="0">0-order model of sequences</option>
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135 <option value="1" selected="True">1st order model of sequences</option>
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136 <option value="2">2nd order model of sequences</option>
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137 <option value="3">3rd order model of sequences</option>
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138 <option value="4">4th order model of sequences</option>
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139 </param>
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140 <param name="nmeme" type="integer" optional="true" value="" min="1" label="Limit of sequences to pass to MEME"/>
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141 <conditional name="subsampling_cond">
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142 <param name="subsampling" type="select" label="Should subsampling be random?" help="Select 'No' if your input sequences are sorted in order of confidence (best to worst)">
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143 <option value="yes" selected="true">Yes</option>
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144 <option value="no">No</option>
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145 </param>
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146 <when value="yes">
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147 <param name="seed" type="integer" optional="true" value="" min="1" label="Seed for the randomized selection of sequences"/>
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148 </when>
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149 <when value="no"/>
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150 </conditional>
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151 <param name="ccut" type="integer" optional="true" value="100" min="0" label="maximum size of a sequence before it is cut down to a centered section" help="Zero value indicates the sequences should not be cut down"/>
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152 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
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153 <param name="group_weak" type="float" optional="true" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/>
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154 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/>
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155 <param name="search_given_strand" type="boolean" truevalue="-norc" falsevalue="" checked="False" label="Search given strand only"/>
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156 <param argument="-old_clustering" type="boolean" truevalue="-old_clustering" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
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157 <param name="meme_mod" type="select" label="What is the expected motif site distribution?">
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158 <option value="oops" selected="True">One occurance per sequence</option>
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159 <option value="zoops">Zero or one occurances per sequence</option>
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160 <option value="anr">Any number of repititions</option>
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161 </param>
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162 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/>
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163 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/>
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164 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/>
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165 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/>
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166 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/>
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167 <param argument="-meme_pal" type="boolean" truevalue="-meme-pal" falsevalue="" checked="False" label="Look for palindromes only"/>
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168 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/>
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169 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" />
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170 </when>
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171 </conditional>
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172 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
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173 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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174 </param>
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175 </inputs>
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176 <outputs>
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177 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/>
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178 </outputs>
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179 <tests>
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180 <test>
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181 <param name="input" value="input1.fasta" ftype="fasta"/>
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182 <param name="non_commercial_use" value="True"/>
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183 <output name="output" file="output1.html" ftype="html" compare="contains"/>
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184 </test>
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185 <test>
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186 <param name="input" value="input1.fasta" ftype="fasta"/>
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187 <param name="sequence_alphabet" value="-rna"/>
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188 <param name="options_type" value="advanced"/>
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189 <param name="background_model_order" value="0"/>
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190 <param name="non_commercial_use" value="True"/>
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191 <output name="output" file="output1.html" ftype="html" compare="contains"/>
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192 </test>
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193 </tests>
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194 <help>
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195 .. class:: warningmark
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196
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197 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
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198 Before using, be sure to review, agree, and comply with the license.**
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199
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200 MWMW-ChIP perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.
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201
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202 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
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203
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204 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
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205 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
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206 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
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207 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
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208 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
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209 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
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210 of occurrences, and description for each motif.
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211
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212 .. class:: infomark
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213
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214 For detailed information on MEME, click here_, or view the license_.
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215
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216 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
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217 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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218
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219 </help>
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220 <citations>
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221 <citation type="doi">10.1093/bioinformatics/btr189</citation>
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222 </citations>
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223 </tool>
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224