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1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
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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>Simple wrapper for makeTagDirectory. Used by findPeaks</description>
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6 <!--<version_command></version_command>-->
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7 <command interpreter="python">makeTagDirectory.py ${tagDir.files_path}
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8 #for $alignF in $alignmentFiles
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9 $alignF.file -f $alignF.file.ext
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10 #end for
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11 -o $tagDir
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12 2> $out_log || echo "Error running homer_makeTagDirectory." >&2
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13
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14 </command>
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15 <inputs>
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16 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
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17 <param type="text" name="options" label="Extra options" value="" help="See below for more options">
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18 <sanitizer>
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19 <valid initial="string.printable">
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20 <remove value="'"/>
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21 <remove value="/"/>
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22 </valid>
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23 <mapping initial="none">
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24 <add source="'" target="__sq__"/>
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25 </mapping>
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26 </sanitizer>
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27 </param>
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28 <repeat name="alignmentFiles" title="Alignment Files">
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29 <param name="file" label="Add file" type="data" format="sam,bed" help="Alignments in SAM or BED format" />
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30 </repeat>
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31 </inputs>
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32 <outputs>
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33 <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
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34 <data format="html" name="tagDir" label="${title} tag directory" />
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35 <data format="txt" name="out_log" label="${title}.log" />
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36 <!--<data format="html" name="html_outfile" label="index" />-->
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37 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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38 </outputs>
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39
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40
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41 <tests>
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42 <!--<test>-->
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43 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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44 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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45 <!--</test>-->
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46 </tests>
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47
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48 <help>
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49
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50 .. class:: infomark
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51
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52 **Homer makeTagDirectory**
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53
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54 For more options, look under: "Command line options"
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55
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56 http://biowhat.ucsd.edu/homer/ngs/tagDir.html
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57
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58 **Parameter list**
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59
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60 Command line options (not all of them are supported)::
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61
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62 Usage: makeTagDirectory <directory> <alignment file 1> [file 2] ... [options]
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63
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64 Creates a platform-independent 'tag directory' for later analysis.
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65 Currently BED, eland, bowtie, and sam files are accepted. The program will try to
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66 automatically detect the alignment format if not specified. Program will also
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67 unzip *.gz, *.bz2, and *.zip files and convert *.bam to sam files on the fly
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68 Existing tag directories can be added or combined to make a new one using -d/-t
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69 If more than one format is needed and the program cannot auto-detect it properly,
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70 make separate tag directories by running the program separately, then combine them.
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71 To perform QC/manipulations on an existing tag directory, add "-update"
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72
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73 Options:
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74 -fragLength <# | given> (Set estimated fragment length - given: use read lengths)
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75 By default treats the sample as a single read ChIP-Seq experiment
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76 -format <X> where X can be: (with column specifications underneath)
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77 bed - BED format files:
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78 (1:chr,2:start,3:end,4:+/- or read name,5:# tags,6:+/-)
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79 -force5th (5th column of BED file contains # of reads mapping to position)
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80 sam - SAM formatted files (use samTools to covert BAMs into SAM if you have BAM)
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81 -unique (keep if there is a single best alignment based on mapq)
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82 -mapq <#> (Minimum mapq for -unique, default: 10, set negative to use AS:i:/XS:i:)
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83 -keepOne (keep one of the best alignments even if others exist)
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84 -keepAll (include all alignments in SAM file)
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85 -mis (Maximum allowed mismatches, default: no limit, uses MD:Z: tag)
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86 bowtie - output from bowtie (run with --best -k 2 options)
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87 (1:read name,2:+/-,3:chr,4:position,5:seq,6:quality,7:NA,8:misInfo)
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88 eland_result - output from basic eland
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89 (1:read name,2:seq,3:code,4:#zeroMM,5:#oneMM,6:#twoMM,7:chr,
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90 8:position,9:F/R,10-:mismatches
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91 eland_export - output from illumina pipeline (22 columns total)
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92 (1-5:read name info,9:sequence,10:quality,11:chr,13:position,14:strand)
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93 eland_extended - output from illumina pipeline (4 columns total)
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94 (1:read name,2:sequence,3:match stats,4:positions[,])
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95 mCpGbed - encode style mCpG reporting in extended BED format, no auto-detect
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96 (1:chr,2:start,3:end,4:name,5:,6:+/-,7:,8:,9:,10:#C,11:#mC)
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97 allC - Lister style output files detailing the read information about all cytosines
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98 (1:chr,2:pos,3:strand,4:context,#mC,#totalC,#C
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99 -minCounts <#> (minimum number of reads to report mC/C ratios, default: 10)
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100 -mCcontext <CG|CHG|CHH|all> (only use C's in this context, default: CG)
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101 HiCsummary - minimal paired-end read mapping information
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102 (1:readname,2:chr1,3:5'pos1,4:strand1,5:chr2,6:5'pos2,7:strand2)
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103 -force5th (5th column of BED file contains # of reads mapping to position)
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104 -d <tag directory> [tag directory 2] ... (add Tag directory to new tag directory)
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105 -t <tag file> [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory)
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106 -single (Create a single tags.tsv file for all "chromosomes" - i.e. if >100 chromosomes)
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107 -update (Use current tag directory for QC/processing, do not parse new alignment files)
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108 -tbp <#> (Maximum tags per bp, default: no maximum)
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109 -precision <1|2|3> (number of decimal places to use for tag totals, default: 1)
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110
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111 GC-bias options:
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112 -genome <genome version> (To see available genomes, use "-genome list")
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113 -or- (for custom genomes):
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114 -genome <path-to-FASTA file or directory of FASTA files>
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115
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116 -checkGC (check Sequence bias, requires "-genome")
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117 -freqStart <#> (offset to start calculating frequency, default: -50)
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118 -freqEnd <#> (distance past fragment length to calculate frequency, default: +50)
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119 -oligoStart <#> (oligo bias start)
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120 -oligoEnd <#> (oligo bias end)
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121 -normGC <target GC profile file> (i.e. tagGCcontent.txt file from control experiment)
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122 Use "-normGC default" to match the genomic GC distribution
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123 -normFixedOligo <oligoFreqFile> (normalize 5' end bias, "-normFixedOligo default" ok)
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124 -minNormRatio <#> (Minimum deflation ratio of tag counts, default: 0.25)
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125 -maxNormRatio <#> (Maximum inflation ratio of tag counts, default: 2.0)
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126 -iterNorm <#> (Sets -max/minNormRatio to 1 and 0, iteratively normalizes such that the
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127 resulting distrubtion is no more than #% different than target, i.e. 0.1,default: off)
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128
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129 Paired-end/HiC options
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130 -illuminaPE (when matching PE reads, assumes last character of read name is 0 or 1)
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131 -removePEbg (remove paired end tags within 1.5x fragment length on same chr)
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132 -PEbgLength <#> (remove PE reads facing on another within this distance, default: 1.5x fragLen)
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133 -restrictionSite <seq> (i.e. AAGCTT for HindIII, assign data < 1.5x fragment length to sites)
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134 Must specify genome sequence directory too. (-rsmis <#> to specify mismatches, def: 0)
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135 -both, -one, -onlyOne, -none (Keeps reads near restriction sites, default: keep all)
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136 -removeSelfLigation (removes reads linking same restriction fragment)
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137 -removeRestrictionEnds (removes reads starting on a restriction fragment)
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138 -assignMidPoint (will place reads in the middle of HindIII fragments)
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139 -restrictionSiteLength <#> (maximum distance from restriction site, default: 1.5x fragLen)
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140 -removeSpikes <size bp> <#> (remove tags from regions with > than # times
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141 the average tags per size bp, suggest "-removeSpikes 10000 5")
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142
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143
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144 </help>
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145 </tool>
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146
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