Mercurial > repos > kevyin > homer
comparison makeTagDirectory.xml @ 28:f0b5827b6051 draft default tip
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author | kevyin |
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date | Thu, 20 Dec 2012 18:28:03 -0500 |
parents | 687df269e597 |
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27:d27851e0cbbd | 28:f0b5827b6051 |
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1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1"> | |
2 <requirements> | |
3 <requirement type="package" version="4.1">homer</requirement> | |
4 </requirements> | |
5 <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description> | |
6 <!--<version_command></version_command>--> | |
7 <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} | |
8 #for $alignF in $alignmentFiles | |
9 $alignF.file -f $alignF.file.ext | |
10 #end for | |
11 -o $tagDir | |
12 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 | |
13 | |
14 </command> | |
15 <inputs> | |
16 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> | |
17 <param type="text" name="options" label="Extra options" value="" help="See below for more options"> | |
18 <sanitizer> | |
19 <valid initial="string.printable"> | |
20 <remove value="'"/> | |
21 <remove value="/"/> | |
22 </valid> | |
23 <mapping initial="none"> | |
24 <add source="'" target="__sq__"/> | |
25 </mapping> | |
26 </sanitizer> | |
27 </param> | |
28 <repeat name="alignmentFiles" title="Alignment Files"> | |
29 <param name="file" label="Add file" type="data" format="sam,bed" help="Alignments in SAM or BED format" /> | |
30 </repeat> | |
31 </inputs> | |
32 <outputs> | |
33 <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />--> | |
34 <data format="html" name="tagDir" label="${title} tag directory" /> | |
35 <data format="txt" name="out_log" label="${title}.log" /> | |
36 <!--<data format="html" name="html_outfile" label="index" />--> | |
37 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> | |
38 </outputs> | |
39 | |
40 | |
41 <tests> | |
42 <!--<test>--> | |
43 <!--<param name="input_file" value="extract_genomic_dna.fa" />--> | |
44 <!--<output name="html_file" file="sample_output.html" ftype="html" />--> | |
45 <!--</test>--> | |
46 </tests> | |
47 | |
48 <help> | |
49 | |
50 .. class:: infomark | |
51 | |
52 **Homer makeTagDirectory** | |
53 | |
54 For more options, look under: "Command line options" | |
55 | |
56 http://biowhat.ucsd.edu/homer/ngs/tagDir.html | |
57 | |
58 **Parameter list** | |
59 | |
60 Command line options (not all of them are supported):: | |
61 | |
62 Usage: makeTagDirectory <directory> <alignment file 1> [file 2] ... [options] | |
63 | |
64 Creates a platform-independent 'tag directory' for later analysis. | |
65 Currently BED, eland, bowtie, and sam files are accepted. The program will try to | |
66 automatically detect the alignment format if not specified. Program will also | |
67 unzip *.gz, *.bz2, and *.zip files and convert *.bam to sam files on the fly | |
68 Existing tag directories can be added or combined to make a new one using -d/-t | |
69 If more than one format is needed and the program cannot auto-detect it properly, | |
70 make separate tag directories by running the program separately, then combine them. | |
71 To perform QC/manipulations on an existing tag directory, add "-update" | |
72 | |
73 Options: | |
74 -fragLength <# | given> (Set estimated fragment length - given: use read lengths) | |
75 By default treats the sample as a single read ChIP-Seq experiment | |
76 -format <X> where X can be: (with column specifications underneath) | |
77 bed - BED format files: | |
78 (1:chr,2:start,3:end,4:+/- or read name,5:# tags,6:+/-) | |
79 -force5th (5th column of BED file contains # of reads mapping to position) | |
80 sam - SAM formatted files (use samTools to covert BAMs into SAM if you have BAM) | |
81 -unique (keep if there is a single best alignment based on mapq) | |
82 -mapq <#> (Minimum mapq for -unique, default: 10, set negative to use AS:i:/XS:i:) | |
83 -keepOne (keep one of the best alignments even if others exist) | |
84 -keepAll (include all alignments in SAM file) | |
85 -mis (Maximum allowed mismatches, default: no limit, uses MD:Z: tag) | |
86 bowtie - output from bowtie (run with --best -k 2 options) | |
87 (1:read name,2:+/-,3:chr,4:position,5:seq,6:quality,7:NA,8:misInfo) | |
88 eland_result - output from basic eland | |
89 (1:read name,2:seq,3:code,4:#zeroMM,5:#oneMM,6:#twoMM,7:chr, | |
90 8:position,9:F/R,10-:mismatches | |
91 eland_export - output from illumina pipeline (22 columns total) | |
92 (1-5:read name info,9:sequence,10:quality,11:chr,13:position,14:strand) | |
93 eland_extended - output from illumina pipeline (4 columns total) | |
94 (1:read name,2:sequence,3:match stats,4:positions[,]) | |
95 mCpGbed - encode style mCpG reporting in extended BED format, no auto-detect | |
96 (1:chr,2:start,3:end,4:name,5:,6:+/-,7:,8:,9:,10:#C,11:#mC) | |
97 allC - Lister style output files detailing the read information about all cytosines | |
98 (1:chr,2:pos,3:strand,4:context,#mC,#totalC,#C | |
99 -minCounts <#> (minimum number of reads to report mC/C ratios, default: 10) | |
100 -mCcontext <CG|CHG|CHH|all> (only use C's in this context, default: CG) | |
101 HiCsummary - minimal paired-end read mapping information | |
102 (1:readname,2:chr1,3:5'pos1,4:strand1,5:chr2,6:5'pos2,7:strand2) | |
103 -force5th (5th column of BED file contains # of reads mapping to position) | |
104 -d <tag directory> [tag directory 2] ... (add Tag directory to new tag directory) | |
105 -t <tag file> [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory) | |
106 -single (Create a single tags.tsv file for all "chromosomes" - i.e. if >100 chromosomes) | |
107 -update (Use current tag directory for QC/processing, do not parse new alignment files) | |
108 -tbp <#> (Maximum tags per bp, default: no maximum) | |
109 -precision <1|2|3> (number of decimal places to use for tag totals, default: 1) | |
110 | |
111 GC-bias options: | |
112 -genome <genome version> (To see available genomes, use "-genome list") | |
113 -or- (for custom genomes): | |
114 -genome <path-to-FASTA file or directory of FASTA files> | |
115 | |
116 -checkGC (check Sequence bias, requires "-genome") | |
117 -freqStart <#> (offset to start calculating frequency, default: -50) | |
118 -freqEnd <#> (distance past fragment length to calculate frequency, default: +50) | |
119 -oligoStart <#> (oligo bias start) | |
120 -oligoEnd <#> (oligo bias end) | |
121 -normGC <target GC profile file> (i.e. tagGCcontent.txt file from control experiment) | |
122 Use "-normGC default" to match the genomic GC distribution | |
123 -normFixedOligo <oligoFreqFile> (normalize 5' end bias, "-normFixedOligo default" ok) | |
124 -minNormRatio <#> (Minimum deflation ratio of tag counts, default: 0.25) | |
125 -maxNormRatio <#> (Maximum inflation ratio of tag counts, default: 2.0) | |
126 -iterNorm <#> (Sets -max/minNormRatio to 1 and 0, iteratively normalizes such that the | |
127 resulting distrubtion is no more than #% different than target, i.e. 0.1,default: off) | |
128 | |
129 Paired-end/HiC options | |
130 -illuminaPE (when matching PE reads, assumes last character of read name is 0 or 1) | |
131 -removePEbg (remove paired end tags within 1.5x fragment length on same chr) | |
132 -PEbgLength <#> (remove PE reads facing on another within this distance, default: 1.5x fragLen) | |
133 -restrictionSite <seq> (i.e. AAGCTT for HindIII, assign data < 1.5x fragment length to sites) | |
134 Must specify genome sequence directory too. (-rsmis <#> to specify mismatches, def: 0) | |
135 -both, -one, -onlyOne, -none (Keeps reads near restriction sites, default: keep all) | |
136 -removeSelfLigation (removes reads linking same restriction fragment) | |
137 -removeRestrictionEnds (removes reads starting on a restriction fragment) | |
138 -assignMidPoint (will place reads in the middle of HindIII fragments) | |
139 -restrictionSiteLength <#> (maximum distance from restriction site, default: 1.5x fragLen) | |
140 -removeSpikes <size bp> <#> (remove tags from regions with > than # times | |
141 the average tags per size bp, suggest "-removeSpikes 10000 5") | |
142 | |
143 | |
144 </help> | |
145 </tool> | |
146 |