homer_findmotifsgenome: homer_findMotifsGenome.xml annotate

annotate homer_findMotifsGenome.xml @ 0:ec974e69e0b5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"

author	iuc
date	Sun, 08 Aug 2021 11:02:42 +0000
parents
children	3126da33847c

rev	line source
0 ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	1 <tool id="homer_findMotifsGenome" name="findMotifsGenome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	2 <description/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	3 <macros>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	4 <import>macros.xml</import>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	5 </macros>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	6 <expand macro="xrefs"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	7 <expand macro="requirements"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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 parents: diff changeset	9 ## Taken from fastqc:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	10 #import re
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	11 #import os
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	12 #set input_name = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	13 ln -s '${input}' '${input_name}' &&
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	14 #set output = $input_name + '_motif'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	15 ## Process the genome:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	16 #if str( $genome.source ) == "installed":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	17 #set genome_file = re.sub('[^\w\-\s]', '_', str($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 parents: diff changeset	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: diff changeset	19 #elif str( $genome.source ) == "preparsed":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	20 #set genome_file = os.path.split(str($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: diff changeset	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 parents: diff changeset	22 #elif str( $genome.source ) == "history":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	23 #set genome_file = re.sub('[^\w\-\s]', '_', str($genome.fasta.name)) + '.fa'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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 parents: diff changeset	25 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	26 ## Command:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	27 findMotifsGenome.pl
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	28 ## Peak:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	29 '${input_name}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	30 ## Genome:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	31 '$genome_file'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	32 ## Ouptut folder:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	33 '${output}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	34 ## Options
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	35 #if str( $genome.source ) == "preparsed":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	36 -preparsedDir '$genome.homer_preparse_source.fields.path'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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 parents: diff changeset	38 -mask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	39 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	40 #if str( $genome.choose_center.center ) == "centered":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	41 -size '$genome.homer_preparse_source.fields.size'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	42 #else
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	45 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	46 #else:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	47 #if $genome.mask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	48 -mask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	49 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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 parents: diff changeset	51 -size given
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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( $genome.fixed_size.choose_center.center ) == "centered":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	54 -size '$genome.fixed_size.size'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	55 #else
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	58 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	59 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	60 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	61 -len '$len'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	62 -S $S
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	63 -mis $mis
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	64 $norevopp
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	65 $nomotif
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	66 $rna
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	67 -mset $motif_options.mset
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	68 $motif_options.basic
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	69 $motif_options.bits
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	70 $motif_options.nocheck
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	71 #if $motif_options.mcheck:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	72 -mcheck '$motif_options.mcheck'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	73 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	74 $motif_options.noknown
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	75 #if $motif_options.mknown:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	76 -mknown '$motif_options.mknown'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	77 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	78 $motif_options.nofacts
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	79 $motif_options.seqlogo
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	80 $advanced.norm
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	81 $advanced.h
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	82 #if str($advanced.N):
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	83 -N $advanced.N
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	84 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	85 -local $advanced.local
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	86 -redundant $advanced.redundant
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	87 -maxN $advanced.maxN
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	88 #if $advanced.maskMotif:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	89 -maskMotif '$advanced.maskMotif'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	90 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	91 #if $advanced.opt:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	92 -opt '$advanced.opt'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	93 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	94 $advanced.rand
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	95 #if $advanced.ref:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	96 -ref '$advanced.ref'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	97 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	98 $advanced.oligo
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	99 #if $advanced.fdr:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	100 -fdr $advanced.fdr
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 #if str( $advanced.homer12.version ) == "homer2":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	103 -nlen '$advanced.homer12.nlen'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	104 -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	105 $advanced.homer12.neutral
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	106 -e '$advanced.homer12.e'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	107 $advanced.homer12.quickMask
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	108 -minlp '$advanced.homer12.minlp'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	109 #elif str( $advanced.homer12.version ) == "homer1":
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	110 -depth '$advanced.homer12.depth'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	111 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	112 #if not $nomotif:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	113 && cp '${output}'/homerResults.html outputHomer.html
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	114 && cp -r '${output}' '${html_homer_file.files_path}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	115 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	116 #if not $motif_options.noknown:
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	117 && cp '${output}'/knownResults.html outputKnown.html
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	118 && cp -r '${output}' '${html_file.files_path}'
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	119 #end if
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	120 ]]></command>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	121 <inputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	122 <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	123 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	124 <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	125 <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	126 <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	127 <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	128 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	129 <when value="preparsed">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	130 <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	131 <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	132 <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	133 <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	134 <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	135 </options>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	136 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	137 <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	138 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	139 <when value="installed">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	140 <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	141 <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	142 <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	143 <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	144 </options>
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 <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	147 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	148 <when value="history">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	149 <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	150 <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	151 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	152 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	153 <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)">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	154 <validator type="regex" message="motif lengths must be comma-separated integers without space">^(\d+,)*(\d+)$</validator>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	155 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	156 <param argument="-S" type="integer" min="1" value="25" label="Number of motifs to find"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	157 <param argument="-mis" type="integer" min="0" value="2" label="Number of mismatches during global optimisation"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	158 <param argument="-norevopp" type="boolean" truevalue="-norevopp" falsevalue="" checked="false" label="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	159 <param argument="-nomotif" type="boolean" truevalue="-nomotif" falsevalue="" checked="false" label="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	160 <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"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	161 <section name="motif_options" title="Known Motif Options/Visualization" expanded="False">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	162 <param argument="-mset" type="select" label="Check against motif collects">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	163 <option value="auto" selected="True">automatic</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	164 <option value="vertebrates">vertebrates</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	165 <option value="insects">insects</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	166 <option value="worms">worms</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	167 <option value="plants">plants</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	168 <option value="yeast">yeast</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	169 <option value="all">all</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	170 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	171 <param argument="-basic" type="boolean" truevalue="-basic" falsevalue="" checked="false" label="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	172 <param argument="-bits" type="boolean" truevalue="-bits" falsevalue="" checked="false" label="Scale sequence logos by information content" help="TODO"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	173 <param argument="-nocheck" type="boolean" truevalue="-nocheck" falsevalue="" checked="false" label="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	174 <param argument="-mcheck" type="data" optional="true" format="txt" label="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	175 <param argument="-noknown" type="boolean" truevalue="-noknown" falsevalue="" checked="false" label="Don't search for known motif enrichment"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	176 <param argument="-mknown" type="data" optional="true" format="txt" label="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	177 <param argument="-nofacts" type="boolean" truevalue="-nofacts" falsevalue="" checked="false" label="Omit humor"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	178 <param argument="-seqlogo" type="boolean" truevalue="-seqlogo" falsevalue="" checked="false" label="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	179 </section>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	180 <section name="advanced" title="Advanced options" expanded="false">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	181 <param name="norm" type="select" label="Sequence normalization options:">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	182 <option value="-gc" selected="true">use GC% for sequence content normalization</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	183 <option value="-cpg">use CpG% instead of GC% for sequence content normalization</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	184 <option value="-noweight">no CG correction</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	185 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	186 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="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	187 <param argument="-N" type="integer" min="0" value="" optional="true" label="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	188 <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."/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	189 <param argument="-redundant" type="float" min="0" max="2" value="2" label="Remove redundant sequences matching greater than # fraction, 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	190 <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"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	191 <param argument="-maskMotif" type="data" format="txt" multiple="true" optional="true" label="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	192 <param argument="-opt" type="data" format="txt" multiple="true" optional="true" label="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	193 <param argument="-rand" type="boolean" truevalue="-rand" falsevalue="" checked="false" label="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	194 <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"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	195 <param argument="-oligo" type="boolean" truevalue="-oligo" falsevalue="" checked="false" label="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	196 <param argument="-fdr" type="integer" min="0" value="" label="Number of randomizations to calculate empirical FDR for de novo discovery" optional="true"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	197 <conditional name="homer12">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	198 <param name="version" type="select" label="Which homer version do you want to use">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	199 <option value="homer2" selected="true">homer2 (default)</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	200 <option value="homer1">homer1 (to force the use of the original homer)</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	201 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	202 <when value="homer2">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	203 <param argument="-nlen" type="integer" min="0" value="3" label="length of lower-order oligos to normalize in background"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	204 <param argument="-nmax" type="integer" min="0" value="160" label="Max normalization iterations"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	205 <param argument="-neutral" type="boolean" truevalue="-neutral" falsevalue="" checked="false" label="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	206 <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"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	207 <param argument="-e" type="float" min="0" max="1" value="0" label="" help="Maximum expected motif instance per bp in random sequence"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	208 <param argument="-quickMask" type="boolean" truevalue="-quickMask" falsevalue="" checked="false" label="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	209 <param argument="-minlp" type="float" value="-10" label="stop looking for motifs when seed logp score gets above this number"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	210 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	211 <when value="homer1">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	212 <param argument="-depth" type="select" label="time spent on local optimization default">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	213 <option value="low">low</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	214 <option value="med" selected="true">med</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	215 <option value="high">high</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	216 <option value="allnight">allnight</option>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	217 </param>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	218 </when>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	219 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	220 </section>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	221 </inputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	222 <outputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	223 <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	224 <filter>motif_options['noknown'] is False</filter>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	225 </data>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	226 <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${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	227 <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	228 </data>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	229 </outputs>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	230 <tests>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	231 <test expect_num_outputs="2">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	232 <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	233 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	234 <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	235 <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	236 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	237 <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	238 <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	239 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	240 <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	241 <has_text text="Total target sequences = 1"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	242 <has_text text="Jaspar"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	243 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	244 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	245 </test>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	246 <test expect_num_outputs="2">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	247 <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	248 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	249 <param name="source" value="history"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	250 <param name="fasta" value="chr2_subset.fa"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	251 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	252 <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	253 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	254 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	255 <has_text text="Total Target Sequences = 40"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	256 <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	257 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	258 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	259 <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	260 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	261 <has_text text="CTCF_peaks_shifted_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	262 <has_text text="Total target sequences = 40"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	263 <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	264 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	265 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	266 </test>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	267 <test expect_num_outputs="2">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	268 <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	269 <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	270 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	271 <param name="source" value="history"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	272 <param name="fasta" value="chr2_subset.fa"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	273 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	274 <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	275 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	276 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	277 <has_text text="Total Target Sequences = 34"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	278 <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	279 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	280 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	281 <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	282 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	283 <has_text text="CTCF_peaks_shifted_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	284 <has_text text="Total target sequences = 34"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	285 <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	286 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	287 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	288 </test>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	289 <test expect_num_outputs="1">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	290 <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	291 <conditional name="genome">
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	292 <param name="source" value="history"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	293 <param name="fasta" value="chr2_subset.fa"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	294 </conditional>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	295 <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	296 <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	297 </section>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	298 <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	299 <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	300 <assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	301 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	302 <has_text text="Total Target Sequences = 40"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	303 <has_text text="RAP26"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	304 </assert_contents>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	305 </output>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	306 </test>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	307 </tests>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	308 <help><![CDATA[
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	309
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	310 .. class:: infomark
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	311
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	312 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	313
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	314 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	315
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	316 Usage::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	317
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	318 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	319
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	320 Example::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	321
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	322 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	323
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	324 Possible Genomes::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	325
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	326 -- or --
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	327 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	328 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	329
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	330 Basic options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	331
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	332 -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	333 -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	334 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	335 -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	336 -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	337 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	338 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	339 -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	340 -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	341 -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	342 -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	343 -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	344 -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	345 -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	346 -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	347
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	348 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	349
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	350 -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	351
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	352 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	353
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	354 -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	355 -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	356 -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	357 -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	358 -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	359 -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	360 -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	361 -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	362 -nofacts (omit humor)
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	363 -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	364
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	365 Sequence normalization options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	366
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	367 -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	368 -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	369 -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	370 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	371
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	372 Advanced options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	373
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	374 -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	375 -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	376 -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	377 -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	378 -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	379 -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	380 -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	381 -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	382 -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	383 -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	384 -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	385 -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	386 -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	387 -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	388 -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	389
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	390 homer2 specific options::
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	391
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	392 -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	393 -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	394 -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	395 -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	396 -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	397 -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	398 -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	399 -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	400 -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	401 -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	402
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	403 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	404
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	405 -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	406 -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	407
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	408
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	409 ]]></help>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	410 <expand macro="citation"/>
ec974e69e0b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289" iuc parents: diff changeset	411 </tool>

Mercurial > repos > iuc > homer_findmotifsgenome

annotate homer_findMotifsGenome.xml @ 0:ec974e69e0b5 draft