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1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.5">
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2 <requirements>
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3 <requirement type="package" version="4.1">homer</requirement>
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4 </requirements>
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5 <description></description>
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6 <!--<version_command></version_command>-->
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7 <command>
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8 annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated
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9 2> $out_log || echo "Error running annotatePeaks." >&2
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10 </command>
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11 <inputs>
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12 <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>
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13 <param name="genome_selector" type="select" label="Genome version">
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14 <option value="hg19" selected="true">hg19</option>
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15 </param>
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16 <param type="text" name="options" label="Extra options" value="" help="See link below for more options">
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17 <sanitizer>
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18 <valid initial="string.printable">
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19 <remove value="'"/>
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20 <remove value="/"/>
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21 </valid>
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22 <mapping initial="none">
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23 <add source="'" target="__sq__"/>
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24 </mapping>
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25 </sanitizer>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <!--<data format="html" name="html_outfile" label="index" />-->
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30 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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31 <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
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32 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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37 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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38 </test>
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39 </tests>
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40
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41 <help>
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42
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43 .. class:: infomark
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44
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45 **Homer annoatePeaks**
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46
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47 More information on accepted formats and options
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48
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49 http://biowhat.ucsd.edu/homer/ngs/annotation.html
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50
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51 TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
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52
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53 **Parameter list**
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54
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55 Command line options (not all of them are supported)::
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56
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57 Usage: annotatePeaks.pl <peak file | tss> <genome version> [additional options...]
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58
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59 Available Genomes (required argument): (name,org,directory,default promoter set)
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60 -- or --
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61 Custom: provide the path to genome FASTA files (directory or single file)
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62
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63 User defined annotation files (default is UCSC refGene annotation):
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64 annotatePeaks.pl accepts GTF (gene transfer formatted) files to annotate positions relative
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65 to custom annotations, such as those from de novo transcript discovery or Gencode.
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66 -gtf <gtf format file> (-gff and -gff3 can work for those files, but GTF is better)
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67
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68 Peak vs. tss/tts/rna mode (works with custom GTF file):
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69 If the first argument is "tss" (i.e. annotatePeaks.pl tss hg18 ...) then a TSS centric
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70 analysis will be carried out. Tag counts and motifs will be found relative to the TSS.
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71 (no position file needed) ["tts" now works too - e.g. 3' end of gene]
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72 ["rna" specifies gene bodies, will automaticall set "-size given"]
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73 NOTE: The default TSS peak size is 4000 bp, i.e. +/- 2kb (change with -size option)
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74 -list <gene id list> (subset of genes to perform analysis [unigene, gene id, accession,
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75 probe, etc.], default = all promoters)
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76 -cTSS <promoter position file i.e. peak file> (should be centered on TSS)
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77
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78 Primary Annotation Options:
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79 -mask (Masked repeats, can also add 'r' to end of genome name)
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80 -m <motif file 1> [motif file 2] ... (list of motifs to find in peaks)
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81 -mscore (reports the highest log-odds score within the peak)
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82 -nmotifs (reports the number of motifs per peak)
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83 -mdist (reports distance to closest motif)
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84 -mfasta <filename> (reports sites in a fasta file - for building new motifs)
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85 -fm <motif file 1> [motif file 2] (list of motifs to filter from above)
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86 -rmrevopp <#> (only count sites found within <#> on both strands once, i.e. palindromic)
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87 -matrix <prefix> (outputs a motif co-occurrence files:
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88 prefix.count.matrix.txt - number of peaks with motif co-occurrence
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89 prefix.ratio.matrix.txt - ratio of observed vs. expected co-occurrence
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90 prefix.logPvalue.matrix.txt - co-occurrence enrichment
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91 prefix.stats.txt - table of pair-wise motif co-occurrence statistics
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92 additional options:
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93 -matrixMinDist <#> (minimum distance between motif pairs - to avoid overlap)
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94 -matrixMaxDist <#> (maximum distance between motif pairs)
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95 -mbed <filename> (Output motif positions to a BED file to load at UCSC (or -mpeak))
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96 -mlogic <filename> (will output stats on common motif orientations)
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97 -d <tag directory 1> [tag directory 2] ... (list of experiment directories to show
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98 tag counts for) NOTE: -dfile <file> where file is a list of directories in first column
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99 -bedGraph <bedGraph file 1> [bedGraph file 2] ... (read coverage counts from bedGraph files)
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100 -wig <wiggle file 1> [wiggle file 2] ... (read coverage counts from wiggle files)
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101 -p <peak file> [peak file 2] ... (to find nearest peaks)
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102 -pdist to report only distance (-pdist2 gives directional distance)
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103 -pcount to report number of peaks within region
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104 -vcf <VCF file> (annotate peaks with genetic variation infomation, one col per individual)
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105 -editDistance (Computes the # bp changes relative to reference)
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106 -individuals <name1> [name2] ... (restrict analysis to these individuals)
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107 -gene <data file> ... (Adds additional data to result based on the closest gene.
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108 This is useful for adding gene expression data. The file must have a header,
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109 and the first column must be a GeneID, Accession number, etc. If the peak
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110 cannot be mapped to data in the file then the entry will be left empty.
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111 -go <output directory> (perform GO analysis using genes near peaks)
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112 -genomeOntology <output directory> (perform genomeOntology analysis on peaks)
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113 -gsize <#> (Genome size for genomeOntology analysis, default: 2e9)
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114
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115 Annotation vs. Histogram mode:
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116 -hist <bin size in bp> (i.e 1, 2, 5, 10, 20, 50, 100 etc.)
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117 The -hist option can be used to generate histograms of position dependent features relative
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118 to the center of peaks. This is primarily meant to be used with -d and -m options to map
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119 distribution of motifs and ChIP-Seq tags. For ChIP-Seq peaks for a Transcription factor
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120 you might want to use the -center option (below) to center peaks on the known motif
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121 ** If using "-size given", histogram will be scaled to each region (i.e. 0-100%), with
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122 the -hist parameter being the number of bins to divide each region into.
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123 Histogram Mode specific Options:
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124 -nuc (calculated mononucleotide frequencies at each position,
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125 Will report by default if extracting sequence for other purposes like motifs)
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126 -di (calculated dinucleotide frequencies at each position)
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127 -histNorm <#> (normalize the total tag count for each region to 1, where <#> is the
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128 minimum tag total per region - use to avoid tag spikes from low coverage
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129 -ghist (outputs profiles for each gene, for peak shape clustering)
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130 -rm <#> (remove occurrences of same motif that occur within # bp)
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131
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132 Peak Centering: (other options are ignored)
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133 -center <motif file> (This will re-center peaks on the specified motif, or remove peak
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134 if there is no motif in the peak. ONLY recentering will be performed, and all other
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135 options will be ignored. This will output a new peak file that can then be reanalyzed
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136 to reveal fine-grain structure in peaks (It is advised to use -size < 200) with this
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137 to keep peaks from moving too far (-mirror flips the position)
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138 -multi (returns genomic positions of all sites instead of just the closest to center)
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139
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140 Advanced Options:
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141 -len <#> / -fragLength <#> (Fragment length, default=auto, might want to set to 0 for RNA)
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142 -size <#> (Peak size[from center of peak], default=inferred from peak file)
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143 -size #,# (i.e. -size -10,50 count tags from -10 bp to +50 bp from center)
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144 -size "given" (count tags etc. using the actual regions - for variable length regions)
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145 -log (output tag counts as log2(x+1+rand) values - for scatter plots)
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146 -sqrt (output tag counts as sqrt(x+rand) values - for scatter plots)
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147 -strand <+|-|both> (Count tags on specific strands relative to peak, default: both)
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148 -pc <#> (maximum number of tags to count per bp, default=0 [no maximum])
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149 -cons (Retrieve conservation information for peaks/sites)
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150 -CpG (Calculate CpG/GC content)
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151 -ratio (process tag values as ratios - i.e. chip-seq, or mCpG/CpG)
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152 -nfr (report nuclesome free region scores instead of tag counts, also -nfrSize <#>)
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153 -norevopp (do not search for motifs on the opposite strand [works with -center too])
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154 -noadj (do not adjust the tag counts based on total tags sequenced)
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155 -norm <#> (normalize tags to this tag count, default=1e7, 0=average tag count in all directories)
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156 -pdist (only report distance to nearest peak using -p, not peak name)
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157 -map <mapping file> (mapping between peak IDs and promoter IDs, overrides closest assignment)
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158 -noann, -nogene (skip genome annotation step, skip TSS annotation)
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159 -homer1/-homer2 (by default, the new version of homer [-homer2] is used for finding motifs)
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160
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161
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162 </help>
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163 </tool>
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164
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