Mercurial > repos > iuc > homer_findmotifsgenome

annotate homer_findMotifsGenome.xml @ 3:4fe92af4542b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af
author iuc
date Thu, 06 Apr 2023 16:22:23 +0000
parents a8f207b43f64
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
4fe92af4542b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af
iuc
parents: 2
diff changeset
1 <tool id="homer_findMotifsGenome" name="findMotifsGenome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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2 <description/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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3 <macros>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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4 <import>macros.xml</import>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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5 </macros>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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6 <expand macro="xrefs"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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7 <expand macro="requirements"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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9 ## Taken from fastqc:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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10 #import re
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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11 #import os
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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12 #set input_name = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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13 ln -s '${input}' '${input_name}' &&
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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14 #set output = $input_name + '_motif'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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15 ## Process the genome:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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16 #if str( $genome.source ) == "installed":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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17 #set genome_file = re.sub('[^\w\-\s]', '_', str($genome.all_fasta_source.fields.value)) + '.fa'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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18 ln -s '$genome.all_fasta_source.fields.path' '$genome_file' &&
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
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19 #elif str( $genome.source ) == "preparsed":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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20 #set genome_file = os.path.split(str($genome.homer_preparse_source.fields.path_fasta))[-1]
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
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21 ln -s '$genome.homer_preparse_source.fields.path_fasta' '$genome_file' &&
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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22 #elif str( $genome.source ) == "history":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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23 #set genome_file = re.sub('[^\w\-\s]', '_', str($genome.fasta.name)) + '.fa'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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24 ln -s '$genome.fasta' '$genome_file' &&
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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25 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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26 ## Command:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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27 findMotifsGenome.pl
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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28 ## Peak:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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29 '${input_name}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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30 ## Genome:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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31 '$genome_file'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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32 ## Ouptut folder:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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33 '${output}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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34 ## Options
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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35 #if str( $genome.source ) == "preparsed":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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36 -preparsedDir '$genome.homer_preparse_source.fields.path'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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37 #if str( $genome.homer_preparse_source.fields.mask ) == 'True':
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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38 -mask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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39 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
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40 #if str( $genome.choose_center.center ) == "centered":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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41 -size '$genome.homer_preparse_source.fields.size'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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42 #else
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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43 #set sizee = int($genome.choose_center.sizes) + int($genome.homer_preparse_source.fields.size)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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44 -size '$genome.choose_center.sizes','${sizee}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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45 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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46 #else:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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47 #if $genome.mask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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48 -mask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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49 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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50 #if $genome.fixed_size.size_fixed == "given":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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51 -size given
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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52 #else:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
53 #if str( $genome.fixed_size.choose_center.center ) == "centered":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
54 -size '$genome.fixed_size.size'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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55 #else
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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56 #set sizee = int($genome.fixed_size.choose_center.sizes) + int($genome.fixed_size.size)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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57 -size '$genome.fixed_size.choose_center.sizes','${sizee}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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58 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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59 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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60 #end if
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
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61 #if str( $background.use ) != "none":
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
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62 -bg '$background.bg'
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
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63 #end if
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
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64 #if str( $background.use ) == "withbg":
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
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65 -keepOverlappingBg
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
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66 #else if str( $background.use ) == "chopify":
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
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67 -chopify
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
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68 #end if
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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69 -len '$len'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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70 -S $S
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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71 -mis $mis
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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72 $norevopp
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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73 $nomotif
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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74 $rna
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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75 -mset $motif_options.mset
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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76 $motif_options.basic
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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77 $motif_options.bits
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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78 $motif_options.nocheck
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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79 #if $motif_options.mcheck:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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80 -mcheck '$motif_options.mcheck'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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81 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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82 $motif_options.noknown
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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83 #if $motif_options.mknown:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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84 -mknown '$motif_options.mknown'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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85 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
86 $motif_options.nofacts
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
87 $motif_options.seqlogo
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
88 $advanced.norm
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
89 $advanced.h
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
90 #if str($advanced.N):
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
91 -N $advanced.N
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
92 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
93 -local $advanced.local
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
94 -redundant $advanced.redundant
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
95 -maxN $advanced.maxN
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
96 #if $advanced.maskMotif:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
97 -maskMotif '$advanced.maskMotif'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
98 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
99 #if $advanced.opt:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
100 -opt '$advanced.opt'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
101 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
102 $advanced.rand
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
103 #if $advanced.ref:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
104 -ref '$advanced.ref'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
105 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
106 $advanced.oligo
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
107 #if $advanced.fdr:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
108 -fdr $advanced.fdr
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
109 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
110 #if str( $advanced.homer12.version ) == "homer2":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
111 -nlen '$advanced.homer12.nlen'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
112 -nmax '$advanced.homer12.nmax'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
113 $advanced.homer12.neutral
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
114 -e '$advanced.homer12.e'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
115 $advanced.homer12.quickMask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
116 -minlp '$advanced.homer12.minlp'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
117 #elif str( $advanced.homer12.version ) == "homer1":
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
118 -homer1
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
119 -depth '$advanced.homer12.depth'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
120 #end if
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
121 #if str( $background.use ) == "none":
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
122 #if not $nomotif:
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
123 && cp '${output}/homerResults.html' outputHomer.html
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
124 && cp -r '${output}' '${html_homer_file.files_path}'
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
125 && cp -r '${output}/homerResults' homerResults
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
126 #end if
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
127 #if not $motif_options.noknown:
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
128 && cp '${output}/knownResults.html' outputKnown.html
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
129 && cp -r '${output}' '${html_file.files_path}'
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
130 && cp -r '${output}/knownResults' knownResults
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
131 #end if
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
132 #else
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
133 && cp '${output}/homerResults.html' outputHomer.html
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
134 && cp -r '${output}' '${html_homer_file.files_path}'
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
135 && cp -r '${output}/homerResults' homerResults
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
136 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
137 ]]></command>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
138 <inputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
139 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
140 <conditional name="genome">
3
4fe92af4542b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af
iuc
parents: 2
diff changeset
141 <param name="source" type="select" label="Will you select a reference genome from your history or use an installed genome?">
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
142 <option value="preparsed">Preparsed (fasta is available and has been preparsed to specific size)</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
143 <option value="installed">Installed (fasta is available but will be preparsed as run time)</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
144 <option value="history">From History (fasta will be preparsed at run time)</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
145 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
146 <when value="preparsed">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
147 <param name="homer_preparse_source" type="select" label="Preparsed FASTA">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
148 <options from_data_table="homer_preparse">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
149 <filter type="sort_by" column="2"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
150 <filter type="static_value" column="version" value="@IDX_VERSION@"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
151 <validator type="no_options" message="No preparsed genomes are available"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
152 </options>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
153 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
154 <expand macro="choose_center"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
155 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
156 <when value="installed">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
157 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
158 <options from_data_table="all_fasta">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
159 <filter type="sort_by" column="2"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
160 <validator type="no_options" message="No references are available"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
161 </options>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
162 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
163 <expand macro="mask_size"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
164 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
165 <when value="history">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
166 <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
167 <expand macro="mask_size"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
168 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
169 </conditional>
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
170 <conditional name="background">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
171 <param name="use" type="select" label="Will you use a background model?" >
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
172 <option value="none" selected="true" >No background model</option>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
173 <option value="model" >Background model with regions removed from target Peak file</option>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
174 <option value="withbg" >Background model with regions not removed from target Peak file</option>
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175 <option value="chopify" >Chop large background model regions to the average size of target Peak file regions</option>
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176 </param>
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177 <when value="none"></when>
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178 <when value="model">
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179 <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file"/>
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180 </when>
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181 <when value="withbg">
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182 <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file"/>
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183 </when>
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184 <when value="chopify">
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185 <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file" />
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186 </when>
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187 </conditional>
0
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188 <param argument="-len" type="text" value="8,10,12" label="comma-separated motif lengths" help="values greater 12 may cause the program to run out of memory - in these cases decrease the number of sequences analyzed (-N), or try analyzing shorter sequence regions (i.e. -size 100)">
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189 <validator type="regex" message="motif lengths must be comma-separated integers without space">^(\d+,)*(\d+)$</validator>
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190 </param>
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191 <param argument="-S" type="integer" min="1" value="25" label="Number of motifs to find"/>
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192 <param argument="-mis" type="integer" min="0" value="2" label="Number of mismatches during global optimisation"/>
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193 <param argument="-norevopp" type="boolean" truevalue="-norevopp" falsevalue="" checked="false" label="Don't search reverse strand for motifs"/>
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194 <param argument="-nomotif" type="boolean" truevalue="-nomotif" falsevalue="" checked="false" label="Don't search for de novo motif enrichment"/>
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195 <param argument="-rna" type="boolean" truevalue="-rna" falsevalue="" checked="false" label="output RNA motif logos and compare to RNA motif database" help="automatically sets -norevopp"/>
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196 <section name="motif_options" title="Known Motif Options/Visualization" expanded="False">
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197 <param argument="-mset" type="select" label="Check against motif collects">
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198 <option value="auto" selected="True">automatic</option>
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199 <option value="vertebrates">vertebrates</option>
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200 <option value="insects">insects</option>
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201 <option value="worms">worms</option>
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202 <option value="plants">plants</option>
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203 <option value="yeast">yeast</option>
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204 <option value="all">all</option>
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205 </param>
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206 <param argument="-basic" type="boolean" truevalue="-basic" falsevalue="" checked="false" label="Just visualize de novo motifs, don't check similarity with known motifs"/>
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207 <param argument="-bits" type="boolean" truevalue="-bits" falsevalue="" checked="false" label="Scale sequence logos by information content" help="TODO"/>
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208 <param argument="-nocheck" type="boolean" truevalue="-nocheck" falsevalue="" checked="false" label="Don't search for de novo vs. known motif similarity"/>
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209 <param argument="-mcheck" type="data" optional="true" format="txt" label="known motifs to check against de novo motifs"/>
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210 <param argument="-noknown" type="boolean" truevalue="-noknown" falsevalue="" checked="false" label="Don't search for known motif enrichment"/>
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211 <param argument="-mknown" type="data" optional="true" format="txt" label="Known motifs to check for enrichment"/>
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212 <param argument="-nofacts" type="boolean" truevalue="-nofacts" falsevalue="" checked="false" label="Omit humor"/>
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213 <param argument="-seqlogo" type="boolean" truevalue="-seqlogo" falsevalue="" checked="false" label="Use weblogo/seqlogo/ghostscript to generate logos, default uses SVG now"/>
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214 </section>
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215 <section name="advanced" title="Advanced options" expanded="false">
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216 <param name="norm" type="select" label="Sequence normalization options:">
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217 <option value="-gc" selected="true">use GC% for sequence content normalization</option>
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218 <option value="-cpg">use CpG% instead of GC% for sequence content normalization</option>
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219 <option value="-noweight">no CG correction</option>
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220 </param>
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221 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Use hypergeometric for p-values, binomial is default"/>
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222 <param argument="-N" type="integer" min="0" value="" optional="true" label="Number of sequences to use for motif finding, default=max(50k, 2x input)"/>
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223 <param argument="-local" type="integer" min="0" value="0" label="local background size in bp for each side of regions" help="0 means no local background."/>
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224 <param argument="-redundant" type="float" min="0" max="2" value="2" label="Remove redundant sequences matching greater than # fraction, i.e. -redundant 0.5"/>
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225 <param argument="-maxN" type="float" min="0" max="1" value="0.7" label="maximum percentage of N's in sequence to consider for motif finding"/>
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226 <param argument="-maskMotif" type="data" format="txt" multiple="true" optional="true" label="motifs to mask before motif finding"/>
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227 <param argument="-opt" type="data" format="txt" multiple="true" optional="true" label="motifs to optimize or change length of"/>
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228 <param argument="-rand" type="boolean" truevalue="-rand" falsevalue="" checked="false" label="randomize target and background sequences labels"/>
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229 <param argument="-ref" optional="true" type="data" format="tabular,bed,encodepeak" label="use file for target and background - first argument is list of peak ids for targets"/>
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230 <param argument="-oligo" type="boolean" truevalue="-oligo" falsevalue="" checked="false" label="Perform analysis of individual oligo enrichment"/>
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231 <param argument="-fdr" type="integer" min="0" value="" label="Number of randomizations to calculate empirical FDR for de novo discovery" optional="true"/>
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232 <conditional name="homer12">
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233 <param name="version" type="select" label="Which homer version do you want to use">
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234 <option value="homer2" selected="true">homer2 (default)</option>
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235 <option value="homer1">homer1 (to force the use of the original homer)</option>
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236 </param>
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237 <when value="homer2">
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238 <param argument="-nlen" type="integer" min="0" value="3" label="length of lower-order oligos to normalize in background"/>
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239 <param argument="-nmax" type="integer" min="0" value="160" label="Max normalization iterations"/>
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240 <param argument="-neutral" type="boolean" truevalue="-neutral" falsevalue="" checked="false" label="weight sequences to neutral frequencies, i.e. 25%, 6.25%, etc."/>
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241 <param argument="-olen" type="integer" min="0" value="" optional="true" label="lower-order oligo normalization for oligo table, use if -nlen isn't working well"/>
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242 <param argument="-e" type="float" min="0" max="1" value="0" label="" help="Maximum expected motif instance per bp in random sequence"/>
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243 <param argument="-quickMask" type="boolean" truevalue="-quickMask" falsevalue="" checked="false" label="skip full masking after finding motifs, similar to original homer"/>
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244 <param argument="-minlp" type="float" value="-10" label="stop looking for motifs when seed logp score gets above this number"/>
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245 </when>
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246 <when value="homer1">
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247 <param argument="-depth" type="select" label="time spent on local optimization default">
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248 <option value="low">low</option>
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249 <option value="med" selected="true">med</option>
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250 <option value="high">high</option>
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251 <option value="allnight">allnight</option>
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252 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
253 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
254 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
255 </section>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
256 </inputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
257 <outputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
258 <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
259 <filter>motif_options['noknown'] is False</filter>
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
260 <filter>background['use'] == "none"</filter>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
261 </data>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
262 <collection name="output_collection_known" type="list" label="${tool.name} on ${on_string}: Known motifs files">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
263 <discover_datasets directory="knownResults" pattern="(?P&lt;designation&gt;.+)\.motif" format="txt" visible="false"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
264 <filter>motif_options['noknown'] is False</filter>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
265 <filter>background['use'] == "none"</filter>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
266 </collection>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
267 <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${tool.name} on ${on_string}: De novo motifs">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
268 <filter>nomotif is False</filter>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
269 </data>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
270 <collection name="output_collection_de_novo" type="list" label="${tool.name} on ${on_string}: De novo motifs files">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
271 <discover_datasets directory="homerResults" pattern="(?P&lt;designation&gt;.+)\.motif" format="txt" visible="false"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
272 <filter>nomotif is False</filter>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
273 </collection>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
274 </outputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
275 <tests>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
276 <test expect_num_outputs="4">
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
277 <param name="input" value="fake_phix_peaks.bed"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
278 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
279 <param name="source" value="installed"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
280 <param name="all_fasta_source" value="phiX174"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
281 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
282 <output name="html_file" file="motif_test1/knownResults.html" ftype="html" lines_diff="2"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
283 <output name="html_homer_file">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
284 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
285 <has_text text="fake_phix_peaks_bed_motif/ - Homer de novo Motif Results"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
286 <has_text text="Total target sequences = 1"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
287 <!-- This is too much impredictible -->
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
288 <!-- <has_text text="Jaspar"/> -->
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
289 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
290 </output>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
291 <output_collection name="output_collection_known" type="list" count="0">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
292 </output_collection>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
293 <output_collection name="output_collection_de_novo" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
294 <element name="motif1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
295 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
296 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
297 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
298 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
299 </output_collection>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
300 </test>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
301 <test expect_num_outputs="4">
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
302 <param name="input" value="CTCF_peaks_shifted.bed"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
303 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
304 <param name="source" value="history"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
305 <param name="fasta" value="chr2_subset.fa.gz"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
306 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
307 <output name="html_file">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
308 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
309 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
310 <has_text text="Total Target Sequences = 24"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
311 <has_text text="CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
312 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
313 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
314 <output name="html_homer_file">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
315 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
316 <has_text text="CTCF_peaks_shifted_bed_motif/ - Homer de novo Motif Results"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
317 <has_text text="Total target sequences = 24"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
318 <has_text_matching expression="CTCF(Zf)|CTCF/MA|BORIS|CTCFL"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
319 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
320 </output>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
321 <output_collection name="output_collection_known" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
322 <element name="known1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
323 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
324 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
325 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
326 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
327 </output_collection>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
328 <output_collection name="output_collection_de_novo" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
329 <element name="motif1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
330 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
331 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
332 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
333 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
334 </output_collection>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
335 </test>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
336 <test expect_num_outputs="4">
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
337 <param name="input" value="CTCF_peaks_shifted.bed"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
338 <param name="mask" value="true"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
339 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
340 <param name="source" value="history"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
341 <param name="fasta" value="chr2_subset.fa.gz"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
342 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
343 <output name="html_file">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
344 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
345 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
346 <has_text text="Total Target Sequences = 18"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
347 <has_text text="CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
348 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
349 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
350 <output name="html_homer_file">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
351 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
352 <has_text text="CTCF_peaks_shifted_bed_motif/ - Homer de novo Motif Results"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
353 <has_text text="Total target sequences = 18"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
354 <!-- This is too much impredictible -->
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
355 <!-- <has_text_matching expression="CTCF(Zf)|CTCF/MA|BORIS|CTCFL|NFATC2"/> -->
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
356 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
357 </output>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
358 <output_collection name="output_collection_known" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
359 <element name="known1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
360 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
361 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
362 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
363 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
364 </output_collection>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
365 <output_collection name="output_collection_de_novo" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
366 <element name="motif1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
367 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
368 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
369 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
370 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
371 </output_collection>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
372 </test>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
373 <test expect_num_outputs="2">
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
374 <param name="input" value="CTCF_peaks_shifted.bed"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
375 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
376 <param name="source" value="history"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
377 <param name="fasta" value="chr2_subset.fa.gz"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
378 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
379 <section name="motif_options">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
380 <param name="mset" value="plants"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
381 </section>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
382 <param name="nomotif" value="true"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
383 <output name="html_file">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
384 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
385 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
386 <has_text text="Total Target Sequences = 24"/>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
387 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
388 </output>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
389 <output_collection name="output_collection_known" type="list" count="0">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
390 </output_collection>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
391 </test>
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
392 <!-- background tests -->
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
393 <test expect_num_outputs="2">
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
394 <param name="input" value="fake_phix_peaks.bed"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
395 <conditional name="genome">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
396 <param name="source" value="installed"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
397 <param name="all_fasta_source" value="phiX174"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
398 </conditional>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
399 <conditional name="background">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
400 <param name="use" value="withbg" />
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
401 <param name="bg" value="fake_phix_peaks.subset.bed" />
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
402 </conditional>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
403 <output name="html_homer_file">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
404 <assert_contents>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
405 <has_text text="HOXB13/MA0901.2/Jaspar(0.948)"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
406 <has_text text="Yeast"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
407 </assert_contents>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
408 </output>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
409 <output_collection name="output_collection_de_novo" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
410 <element name="motif1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
411 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
412 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
413 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
414 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
415 </output_collection>
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
416 </test>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
417 <test expect_num_outputs="2">
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
418 <param name="input" value="fake_phix_peaks.bed"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
419 <conditional name="genome">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
420 <param name="source" value="installed"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
421 <param name="all_fasta_source" value="phiX174"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
422 </conditional>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
423 <conditional name="background">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
424 <param name="use" value="chopify" />
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
425 <param name="bg" value="fake_phix_peaks.subset.bed" />
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
426 </conditional>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
427 <output name="html_homer_file">
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
428 <assert_contents>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
429 <has_text text="CCA"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
430 <has_text text="YAP5"/>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
431 </assert_contents>
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
432 </output>
2
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
433 <output_collection name="output_collection_de_novo" type="list">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
434 <element name="motif1">
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
435 <assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
436 <has_text text=">"/>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
437 </assert_contents>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
438 </element>
a8f207b43f64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
iuc
parents: 1
diff changeset
439 </output_collection>
1
3126da33847c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
iuc
parents: 0
diff changeset
440 </test>
0
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
441 </tests>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
442 <help><![CDATA[
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
443
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
444 .. class:: infomark
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
445
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
446 This is a wrapper for findMotifsGenome.pl from HOMER but not all options are included.
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
447
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
448 Program will find de novo and known motifs in regions in the genome.
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
449
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
450 Usage::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
451
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
452 findMotifsGenome.pl <pos file> <genome> <output directory> [additional options]
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
453
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
454 Example::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
455
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
456 findMotifsGenome.pl peaks.txt mm8r peakAnalysis -size 200 -len 8
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
457
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
458 Possible Genomes::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
459
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
460 -- or --
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
461 Custom: provide the path to genome FASTA files (directory or single file)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
462 Heads up: will create the directory "preparsed/" in same location.
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
463
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
464 Basic options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
465
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
466 -mask (mask repeats/lower case sequence, can also add 'r' to genome, i.e. mm9r)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
467 -bg <background position file> (genomic positions to be used as background, default=automatic)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
468 removes background positions overlapping with target positions unless -keepOverlappingBg is used
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
469 -chopify (chop up large background regions to the avg size of target regions)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
470 -len <#>[,<#>,<#>...] (motif length, default=8,10,12) [NOTE: values greater 12 may cause the program
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
471 to run out of memory - in these cases decrease the number of sequences analyzed (-N),
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
472 or try analyzing shorter sequence regions (i.e. -size 100)]
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
473 -size <#> (fragment size to use for motif finding, default=200)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
474 -size <#,#> (i.e. -size -100,50 will get sequences from -100 to +50 relative from center)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
475 -size given (uses the exact regions you give it)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
476 -S <#> (Number of motifs to optimize, default: 25)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
477 -mis <#> (global optimization: searches for strings with # mismatches, default: 2)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
478 -norevopp (don't search reverse strand for motifs)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
479 -nomotif (don't search for de novo motif enrichment)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
480 -rna (output RNA motif logos and compare to RNA motif database, automatically sets -norevopp)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
481
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
482 Scanning sequence for motifs::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
483
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
484 -find <motif file> (This will cause the program to only scan for motifs)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
485
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
486 Known Motif Options/Visualization::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
487
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
488 -mset <vertebrates|insects|worms|plants|yeast|all> (check against motif collects, default: auto)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
489 -basic (just visualize de novo motifs, don't check similarity with known motifs)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
490 -bits (scale sequence logos by information content, default: doesn't scale)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
491 -nocheck (don't search for de novo vs. known motif similarity)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
492 -mcheck <motif file> (known motifs to check against de novo motifs,
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
493 -float (allow adjustment of the degeneracy threshold for known motifs to improve p-value[dangerous])
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
494 -noknown (don't search for known motif enrichment, default: -known)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
495 -mknown <motif file> (known motifs to check for enrichment,
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
496 -nofacts (omit humor)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
497 -seqlogo (use weblogo/seqlogo/ghostscript to generate logos, default uses SVG now)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
498
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
499 Sequence normalization options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
500
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
501 -gc (use GC% for sequence content normalization, now the default)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
502 -cpg (use CpG% instead of GC% for sequence content normalization)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
503 -noweight (no CG correction)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
504 Also -nlen <#>, -olen <#>, see homer2 section below.
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
505
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
506 Advanced options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
507
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
508 -h (use hypergeometric for p-values, binomial is default)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
509 -N <#> (Number of sequences to use for motif finding, default=max(50k, 2x input)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
510 -local <#> (use local background, # of equal size regions around peaks to use i.e. 2)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
511 -redundant <#> (Remove redundant sequences matching greater than # percent, i.e. -redundant 0.5)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
512 -maxN <#> (maximum percentage of N's in sequence to consider for motif finding, default: 0.7)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
513 -maskMotif <motif file1> [motif file 2]... (motifs to mask before motif finding)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
514 -opt <motif file1> [motif file 2]... (motifs to optimize or change length of)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
515 -rand (randomize target and background sequences labels)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
516 -ref <peak file> (use file for target and background - first argument is list of peak ids for targets)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
517 -oligo (perform analysis of individual oligo enrichment)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
518 -dumpFasta (Dump fasta files for target and background sequences for use with other programs)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
519 -preparse (force new background files to be created)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
520 -preparsedDir <directory> (location to search for preparsed file and/or place new files)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
521 -keepFiles (keep temporary files)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
522 -fdr <#> (Calculate empirical FDR for de novo discovery #=number of randomizations)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
523
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
524 homer2 specific options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
525
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
526 -homer2 (use homer2 instead of original homer, default)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
527 -nlen <#> (length of lower-order oligos to normalize in background, default: -nlen 3)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
528 -nmax <#> (Max normalization iterations, default: 160)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
529 -neutral (weight sequences to neutral frequencies, i.e. 25%, 6.25%, etc.)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
530 -olen <#> (lower-order oligo normalization for oligo table, use if -nlen isn't working well)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
531 -p <#> (Number of processors to use, default: 1)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
532 -e <#> (Maximum expected motif instance per bp in random sequence, default: 0.01)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
533 -cache <#> (size in MB for statistics cache, default: 500)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
534 -quickMask (skip full masking after finding motifs, similar to original homer)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
535 -minlp <#> (stop looking for motifs when seed logp score gets above #, default: -10)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
536
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
537 Original homer specific options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
538
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
539 -homer1 (to force the use of the original homer)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
540 -depth [low|med|high|allnight] (time spent on local optimization default: med)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
541
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
542
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
543 ]]></help>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
544 <expand macro="citation"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
545 </tool>