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Changeset 19:251442d07ef8 (2012-12-19)

Previous changeset 18:6f1302d12a38 (2012-12-19) Next changeset 20:90db049d8f68 (2012-12-19)

Commit message:
Deleted selected files

removed:
README
annotatePeaks.xml
bed2pos.xml
findPeaks.xml
makeTagDirectory.py
makeTagDirectory.xml
pos2bed.xml
tool_dependencies.xml

diff -r 6f1302d12a38 -r 251442d07ef8 README
--- a/README Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,13 +0,0 @@
-Homer wrapper for Galaxy
-
-Code repo: https://bitbucket.org/gvl/homer
-
-=========================================:
-LICENSE for this wrapper:
-=========================================:
-Kevin Ying
-Garvan Institute: http://www.garvan.org.au
-GVL: https://genome.edu.au/wiki/GVL
-
-http://opensource.org/licenses/mit-license.php
-

diff -r 6f1302d12a38 -r 251442d07ef8 annotatePeaks.xml
--- a/annotatePeaks.xml Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,164 +0,0 @@\n-<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4">\n- <requirements>\n- <requirement type="package" version="4.1">homer</requirement>\n- </requirements>\n- <description></description>\n- \n- <command>\n- annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated\n- 2> $out_log || echo "Error running annotatePeaks." >&2\n- </command>\n- <inputs>\n- <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>\n- <param name="genome_selector" type="select" label="Genome version">\n- <option value="hg19" selected="true">hg19</option>\n- </param>\n- <param type="text" name="options" label="Extra options" value="" help="See link below for more options">\n- <sanitizer>\n- <valid initial="string.printable">\n- <remove value="'"/>\n- <remove value="/"/>\n- </valid>\n- <mapping initial="none">\n- <add source="'" target="__sq__"/>\n- </mapping>\n- </sanitizer>\n- </param>\n- </inputs>\n- <outputs>\n- \n- \n- <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />\n- <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />\n- </outputs>\n- <tests>\n- <test>\n- \n- \n- </test>\n- </tests>\n-\n- <help>\n-\n- .. class:: infomark\n-\n- **Homer annoatePeaks**\n-\n- More information on accepted formats and options\n-\n- http://biowhat.ucsd.edu/homer/ngs/annotation.html\n-\n- TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.\n-\n-**Parameter list**\n-\n-Command line options (not all of them are supported)::\n-\n-\tUsage: annotatePeaks.pl <peak file | tss> <genome version> [additional options...]\n-\n-\tAvailable Genomes (required argument): (name,org,directory,default promoter set)\n-\t\t\t-- or --\n-\t\tCustom: provide the path to genome FASTA files (directory or single file)\n-\n-\tUser defined annotation files (default is UCSC refGene annotation):\n-\t\tannotatePeaks.pl accepts GTF (gene transfer formatted) files to annotate positions relative\n-\t\tto custom annotations, such as those from de novo transcript discovery or Gencode.\n-\t\t-gtf <gtf format file> (-gff and -gff3 can work for those files, but GTF is better)\n-\n-\tPeak vs. tss/tts/rna mode (works with custom GTF file):\n-\t\tIf the first argument is "tss" (i.e. annotatePeaks.pl tss hg18 ...) then a TSS centric\n-\t\tanalysis will be carried out. Tag counts and motifs will be found relative to the TSS.\n-\t\t(no position file needed) ["tts" now works too - e.g. 3' end of gene]\n-\t\t["rna" specifies gene bodies, will automaticall set "-size given"]\n-\t\tNOTE: The default TSS peak size is 4000 bp, i.e. +/- 2kb (change with -size option)\n-\t\t-list <gene id list> (subset of genes to perform analysis [unigene, gene id, accession,\n-\t\t\t probe, etc.], default = all promoters)\n-\t\t-cTSS <promoter position file i.e. peak file> (should be centered on TSS)\n-\n-\tPrimary Annotation Options:\n-\t\t-mask (Masked repeats, can also add 'r' to end of genome name)\n-\t\t-m <motif file 1> [motif file 2] ... (list of motifs to find in peaks)\n-\t\t\t-mscore (reports the highest log-odds score within the peak)\n-\t\t\t-nmotifs (reports the number of motifs per peak)\n-\t\t\t-mdist (reports di'..b' analysis to these individuals)\n-\t\t-gene <data file> ... (Adds additional data to result based on the closest gene.\n-\t\t\tThis is useful for adding gene expression data. The file must have a header,\n-\t\t\tand the first column must be a GeneID, Accession number, etc. If the peak\n-\t\t\tcannot be mapped to data in the file then the entry will be left empty.\n-\t\t-go <output directory> (perform GO analysis using genes near peaks)\n-\t\t-genomeOntology <output directory> (perform genomeOntology analysis on peaks)\n-\t\t\t-gsize <#> (Genome size for genomeOntology analysis, default: 2e9)\n-\n-\tAnnotation vs. Histogram mode:\n-\t\t-hist <bin size in bp> (i.e 1, 2, 5, 10, 20, 50, 100 etc.)\n-\t\tThe -hist option can be used to generate histograms of position dependent features relative\n-\t\tto the center of peaks. This is primarily meant to be used with -d and -m options to map\n-\t\tdistribution of motifs and ChIP-Seq tags. For ChIP-Seq peaks for a Transcription factor\n-\t\tyou might want to use the -center option (below) to center peaks on the known motif\n-\t\t** If using "-size given", histogram will be scaled to each region (i.e. 0-100%), with\n-\t\tthe -hist parameter being the number of bins to divide each region into.\n-\t\t\tHistogram Mode specific Options:\n-\t\t\t-nuc (calculated mononucleotide frequencies at each position,\n-\t\t\t\tWill report by default if extracting sequence for other purposes like motifs)\n-\t\t\t-di (calculated dinucleotide frequencies at each position)\n-\t\t\t-histNorm <#> (normalize the total tag count for each region to 1, where <#> is the\n-\t\t\t\tminimum tag total per region - use to avoid tag spikes from low coverage\n-\t\t\t-ghist (outputs profiles for each gene, for peak shape clustering)\n-\t\t\t-rm <#> (remove occurrences of same motif that occur within # bp)\n-\n-\tPeak Centering: (other options are ignored)\n-\t\t-center <motif file> (This will re-center peaks on the specified motif, or remove peak\n-\t\t\tif there is no motif in the peak. ONLY recentering will be performed, and all other\n-\t\t\toptions will be ignored. This will output a new peak file that can then be reanalyzed\n-\t\t\tto reveal fine-grain structure in peaks (It is advised to use -size < 200) with this\n-\t\t\tto keep peaks from moving too far (-mirror flips the position)\n-\t\t-multi (returns genomic positions of all sites instead of just the closest to center)\n-\n-\tAdvanced Options:\n-\t\t-len <#> / -fragLength <#> (Fragment length, default=auto, might want to set to 0 for RNA)\n-\t\t-size <#> (Peak size[from center of peak], default=inferred from peak file)\n-\t\t\t-size #,# (i.e. -size -10,50 count tags from -10 bp to +50 bp from center)\n-\t\t\t-size "given" (count tags etc. using the actual regions - for variable length regions)\n-\t\t-log (output tag counts as log2(x+1+rand) values - for scatter plots)\n-\t\t-sqrt (output tag counts as sqrt(x+rand) values - for scatter plots)\n-\t\t-strand <+|-|both> (Count tags on specific strands relative to peak, default: both)\n-\t\t-pc <#> (maximum number of tags to count per bp, default=0 [no maximum])\n-\t\t-cons (Retrieve conservation information for peaks/sites)\n-\t\t-CpG (Calculate CpG/GC content)\n-\t\t-ratio (process tag values as ratios - i.e. chip-seq, or mCpG/CpG)\n-\t\t-nfr (report nuclesome free region scores instead of tag counts, also -nfrSize <#>)\n-\t\t-norevopp (do not search for motifs on the opposite strand [works with -center too])\n-\t\t-noadj (do not adjust the tag counts based on total tags sequenced)\n-\t\t-norm <#> (normalize tags to this tag count, default=1e7, 0=average tag count in all directories)\n-\t\t-pdist (only report distance to nearest peak using -p, not peak name)\n-\t\t-map <mapping file> (mapping between peak IDs and promoter IDs, overrides closest assignment)\n-\t\t-noann, -nogene (skip genome annotation step, skip TSS annotation)\n-\t\t-homer1/-homer2 (by default, the new version of homer [-homer2] is used for finding motifs)\n-\n-\n- </help>\n-</tool>\n-\n'

diff -r 6f1302d12a38 -r 251442d07ef8 bed2pos.xml
--- a/bed2pos.xml Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,37 +0,0 @@
-<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.3">
-    <requirements>
-        <requirement type="package" version="4.1">homer</requirement>
-    </requirements>
-    <description></description>
-    
-    <command>
-        bed2pos.pl $input_bed 1> $out_pos
-        2> $out_log || echo "Error running bed2pos." >&2
-    </command>
-    <inputs>
-        <param format="tabular,bed" name="input_bed" type="data" label="BED file" />
-    </inputs>
-    <outputs>
-        
-        
-        <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            
-            
-        </test>
-    </tests>
-
-    <help>
-        .. class:: infomark
-
-        Converts: BED -(to)-> homer peak positions
-
-        **Homer bed2pos.pl**
-
-        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
-    </help>
-</tool>
-

diff -r 6f1302d12a38 -r 251442d07ef8 findPeaks.xml
--- a/findPeaks.xml Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,122 +0,0 @@
-<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2">
-    <requirements>
-        <requirement type="package" version="4.1">homer</requirement>
-    </requirements>
-    <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description>
-    
-    <command>
-        findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
-
-    #if $control_tagDir:
-        -i $control_tagDir.extra_files_path
-    #end if
-
-        2> $out_log || echo "Error running findPeaks." >&2
-    </command>
-    <inputs>
-        <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" />
-        <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" />
-        <param type="text" name="options" label="Extra options" value="" help="See link below for more options">
-          <sanitizer>
-            <valid initial="string.printable">
-             <remove value="'"/>
-             <remove value="/"/>
-            </valid>
-            <mapping initial="none">
-              <add source="'" target="__sq__"/>
-            </mapping>
-          </sanitizer>
-        </param>
-    </inputs>
-    <outputs>
-        
-        
-        <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            
-            
-        </test>
-    </tests>
-
-    <help>
-
-  .. class:: infomark
-
-  **Homer findPeaks**
-
-  For more options, look under: "Command line options for findPeaks"
-
-  http://biowhat.ucsd.edu/homer/ngs/peaks.html
-
-  TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
-
-**Parameter list**
-
-Command line options (not all of them are supported)::
-
- Usage: findPeaks <tag directory> [options]
-
- Finds peaks in the provided tag directory.  By default, peak list printed to stdout
-
- General analysis options:
- -o <filename|auto> (file name for to output peaks, default: stdout)
- "-o auto" will send output to "<tag directory>/peaks.txt", ".../regions.txt",
- or ".../transcripts.txt" depending on the "-style" option
- -style <option> (Specialized options for specific analysis strategies)
- factor (transcription factor ChIP-Seq, uses -center, output: peaks.txt,  default)
- histone (histone modification ChIP-Seq, region based, uses -region -size 500 -L 0, regions.txt)
- groseq (de novo transcript identification from GroSeq data, transcripts.txt)
- tss (TSS identification from 5' RNA sequencing, tss.txt)
- dnase (Hypersensitivity [crawford style (nicking)], peaks.txt)
-
- chipseq/histone options:
- -i <input tag directory> (Experiment to use as IgG/Input/Control)
- -size <#> (Peak size, default: auto)
- -minDist <#> (minimum distance between peaks, default: peak size x2)
- -gsize <#> (Set effective mappable genome size, default: 2e9)
- -fragLength <#|auto> (Approximate fragment length, default: auto)
- -inputFragLength <#|auto> (Approximate fragment length of input tags, default: auto)
- -tbp <#> (Maximum tags per bp to count, 0 = no limit, default: auto)
- -inputtbp <#> (Maximum tags per bp to count in input, 0 = no limit, default: auto)
- -strand <both|separate> (find peaks using tags on both strands or separate, default:both)
- -norm # (Tag count to normalize to, default 10000000)
- -region (extends start/stop coordinates to cover full region considered "enriched")
- -center (Centers peaks on maximum tag overlap and calculates focus ratios)
- -nfr (Centers peaks on most likely nucleosome free region [works best with mnase data])
- (-center and -nfr can be performed later with "getPeakTags"
-
- Peak Filtering options: (set -F/-L/-C to 0 to skip)
- -F <#> (fold enrichment over input tag count, default: 4.0)
-   -P <#> (poisson p-value threshold relative to input tag count, default: 0.0001)
- -L <#> (fold enrichment over local tag count, default: 4.0)
-   -LP <#> (poisson p-value threshold relative to local tag count, default: 0.0001)
- -C <#> (fold enrichment limit of expected unique tag positions, default: 2.0)
- -localSize <#> (region to check for local tag enrichment, default: 10000)
- -inputSize <#> (Size of region to search for control tags, default: 2x peak size)
- -fdr <#> (False discovery rate, default = 0.001)
- -poisson <#> (Set poisson p-value cutoff, default: uses fdr)
- -tagThreshold <#> (Set # of tags to define a peak, default: 25)
- -ntagThreshold <#> (Set # of normalized tags to define a peak, by default uses 1e7 for norm)
- -minTagThreshold <#> (Absolute minimum tags per peak, default: expected tags per peak)
-
- GroSeq Options: (Need to specify "-style groseq"):
- -tssSize <#> (size of region for initiation detection/artifact size, default: 250)
- -minBodySize <#> (size of regoin for transcript body detection, default: 1000)
- -maxBodySize <#> (size of regoin for transcript body detection, default: 10000)
- -tssFold <#> (fold enrichment for new initiation dectection, default: 4.0)
- -bodyFold <#> (fold enrichment for new transcript dectection, default: 4.0)
- -endFold <#> (end transcript when levels are this much less than the start, default: 10.0)
- -fragLength <#> (Approximate fragment length, default: 150)
- -uniqmap <directory> (directory of binary files specifying uniquely mappable locations)
- Download from http://biowhat.ucsd.edu/homer/groseq/
- -confPvalue <#> (confidence p-value: 1.00e-05)
- -minReadDepth <#> (Minimum initial read depth for transcripts, default: auto)
- -pseudoCount <#> (Pseudo tag count, default: 2.0)
- -gtf <filename> (Output de novo transcripts in GTF format)
- "-o auto" will produce <dir>/transcripts.txt and <dir>/transcripts.gtf
-    </help>
-</tool>
-

diff -r 6f1302d12a38 -r 251442d07ef8 makeTagDirectory.py
--- a/makeTagDirectory.py Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,94 +0,0 @@
-"""
-
-
-"""
-import re
-import os
-import sys
-import subprocess
-import optparse
-import shutil
-import tempfile
-
-def getFileString(fpath, outpath):
-    """
-    format a nice file size string
-    """
-    size = ''
-    fp = os.path.join(outpath, fpath)
-    s = '? ?'
-    if os.path.isfile(fp):
-        n = float(os.path.getsize(fp))
-        if n > 2**20:
-            size = ' (%1.1f MB)' % (n/2**20)
-        elif n > 2**10:
-            size = ' (%1.1f KB)' % (n/2**10)
-        elif n > 0:
-            size = ' (%d B)' % (int(n))
-        s = '%s %s' % (fpath, size)
-    return s
-
-class makeTagDirectory():
-    """wrapper
-    """
-
-    def __init__(self,opts=None, args=None):
-        self.opts = opts
-        self.args = args
-
-    def run_makeTagDirectory(self):
-        """
-        makeTagDirectory <Output Directory Name> [options] <alignment file1> [alignment file 2]
-
-        """
-        if self.opts.format != "bam":
-            cl = [self.opts.executable] + args + ["-format" , self.opts.format]
-        else:
-            cl = [self.opts.executable] + args
-        print cl
-        p = subprocess.Popen(cl)
-        retval = p.wait()
-
-
-        html = self.gen_html(args[0])
-        #html = self.gen_html()
-        return html,retval
-
-    def gen_html(self, dr=os.getcwd()):
-        flist = os.listdir(dr)
-        print flist
-        """ add a list of all files in the tagdirectory
-        """
-        res = ['<div class="module"><h2>Files created by makeTagDirectory</h2><table cellspacing="2" cellpadding="2">\n']
-
-        flist.sort()
-        for i,f in enumerate(flist):
-             if not(os.path.isdir(f)):
-                 fn = os.path.split(f)[-1]
-                 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, dr)))
-
-        res.append('</table>\n')
-
-        return res
-
-if __name__ == '__main__':
-    op = optparse.OptionParser()
-    op.add_option('-e', '--executable', default='makeTagDirectory')
-    op.add_option('-o', '--htmloutput', default=None)
-    op.add_option('-f', '--format', default="sam")
-    opts, args = op.parse_args()
-    #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable
-
-    #if not os.path.exists(opts.outputdir):
-        #os.makedirs(opts.outputdir)
-    f = makeTagDirectory(opts, args)
-
-    html,retval = f.run_makeTagDirectory()
-    f = open(opts.htmloutput, 'w')
-    f.write(''.join(html))
-    f.close()
-    if retval <> 0:
-         print >> sys.stderr, serr # indicate failure
-
-
-

diff -r 6f1302d12a38 -r 251442d07ef8 makeTagDirectory.xml
--- a/makeTagDirectory.xml Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,146 +0,0 @@\n-<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">\n- <requirements>\n- <requirement type="package" version="4.1">homer</requirement>\n- </requirements>\n- <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description>\n- \n- <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} \n- #for $alignF in $alignmentFiles\n- $alignF.file -f $alignF.file.ext\n- #end for\n- -o $tagDir\n- 2> $out_log || echo "Error running homer_makeTagDirectory." >&2\n-\n- </command>\n- <inputs>\n- <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />\n- <param type="text" name="options" label="Extra options" value="" help="See below for more options">\n- <sanitizer>\n- <valid initial="string.printable">\n- <remove value="'"/>\n- <remove value="/"/>\n- </valid>\n- <mapping initial="none">\n- <add source="'" target="__sq__"/>\n- </mapping>\n- </sanitizer>\n- </param>\n- <repeat name="alignmentFiles" title="Alignment Files">\n- <param name="file" label="Add file" type="data" format="sam,bed" help="Alignments in SAM or BED format" />\n- </repeat>\n- </inputs>\n- <outputs>\n- \n- <data format="html" name="tagDir" label="${title} tag directory" />\n- <data format="txt" name="out_log" label="${title}.log" />\n- \n- \n- </outputs>\n-\n-\n- <tests>\n- \n- \n- \n- \n- </tests>\n-\n- <help>\n-\n- .. class:: infomark\n-\n- **Homer makeTagDirectory**\n-\n- For more options, look under: "Command line options"\n-\n- http://biowhat.ucsd.edu/homer/ngs/tagDir.html\n-\n-**Parameter list**\n-\n-Command line options (not all of them are supported)::\n-\n-\tUsage: makeTagDirectory <directory> <alignment file 1> [file 2] ... [options]\n-\n-\tCreates a platform-independent 'tag directory' for later analysis.\n-\tCurrently BED, eland, bowtie, and sam files are accepted. The program will try to\n-\tautomatically detect the alignment format if not specified. Program will also\n-\tunzip *.gz, *.bz2, and *.zip files and convert *.bam to sam files on the fly\n-\tExisting tag directories can be added or combined to make a new one using -d/-t\n-\tIf more than one format is needed and the program cannot auto-detect it properly,\n-\tmake separate tag directories by running the program separately, then combine them.\n-\tTo perform QC/manipulations on an existing tag directory, add "-update"\n-\n-\tOptions:\n-\t\t-fragLength <# | given> (Set estimated fragment length - given: use read lengths)\n-\t\t\tBy default treats the sample as a single read ChIP-Seq experiment\n-\t\t-format <X> where X can be: (with column specifications underneath)\n-\t\t\tbed - BED format files:\n-\t\t\t\t(1:chr,2:start,3:end,4:+/- or read name,5:# tags,6:+/-)\n-\t\t\t\t-force5th (5th column of BED file contains # of reads mapping to position)\n-\t\t\tsam - SAM formatted files (use samTools to covert BAMs into SAM if you have BAM)\n-\t\t\t\t-unique (keep if there is a single best alignment based on mapq)\n-\t\t\t\t\t-mapq <#> (Minimum mapq for -unique, default: 10, set negative to use AS:i:/XS:i:)\n-\t\t\t\t-keepOne (keep one of the best alignments even if others exist)\n-\t\t\t\t-keepAll (include all alignments in SAM file)\n-\t\t\t\t-mis (Maximum allowed mismatches, default: no limit, uses MD:Z: tag)\n-\t\t\tbowtie - o'..b'st -k 2 options)\n-\t\t\t\t(1:read name,2:+/-,3:chr,4:position,5:seq,6:quality,7:NA,8:misInfo)\n-\t\t\teland_result - output from basic eland\n-\t\t\t\t(1:read name,2:seq,3:code,4:#zeroMM,5:#oneMM,6:#twoMM,7:chr,\n-\t\t\t\t\t\t\t8:position,9:F/R,10-:mismatches\n-\t\t\teland_export - output from illumina pipeline (22 columns total)\n-\t\t\t\t(1-5:read name info,9:sequence,10:quality,11:chr,13:position,14:strand)\n-\t\t\teland_extended - output from illumina pipeline (4 columns total)\n-\t\t\t\t(1:read name,2:sequence,3:match stats,4:positions[,])\n-\t\t\tmCpGbed - encode style mCpG reporting in extended BED format, no auto-detect\n-\t\t\t\t(1:chr,2:start,3:end,4:name,5:,6:+/-,7:,8:,9:,10:#C,11:#mC)\n-\t\t\tallC - Lister style output files detailing the read information about all cytosines\n-\t\t\t\t(1:chr,2:pos,3:strand,4:context,#mC,#totalC,#C\n-\t\t\t\t-minCounts <#> (minimum number of reads to report mC/C ratios, default: 10)\n-\t\t\t\t-mCcontext <CG|CHG|CHH|all> (only use C's in this context, default: CG)\n-\t\t\tHiCsummary - minimal paired-end read mapping information\n-\t\t\t\t(1:readname,2:chr1,3:5'pos1,4:strand1,5:chr2,6:5'pos2,7:strand2)\n-\t\t-force5th (5th column of BED file contains # of reads mapping to position)\n-\t\t-d <tag directory> [tag directory 2] ... (add Tag directory to new tag directory)\n-\t\t-t <tag file> [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory)\n-\t\t-single (Create a single tags.tsv file for all "chromosomes" - i.e. if >100 chromosomes)\n-\t\t-update (Use current tag directory for QC/processing, do not parse new alignment files)\n-\t\t-tbp <#> (Maximum tags per bp, default: no maximum)\n-\t\t-precision <1|2|3> (number of decimal places to use for tag totals, default: 1)\n-\n-\t\tGC-bias options:\n-\t\t-genome <genome version> (To see available genomes, use "-genome list")\n-\t\t\t-or- (for custom genomes):\n-\t\t-genome <path-to-FASTA file or directory of FASTA files>\n-\n-\t\t-checkGC (check Sequence bias, requires "-genome")\n-\t\t\t-freqStart <#> (offset to start calculating frequency, default: -50)\n-\t\t\t-freqEnd <#> (distance past fragment length to calculate frequency, default: +50)\n-\t\t\t-oligoStart <#> (oligo bias start)\n-\t\t\t-oligoEnd <#> (oligo bias end)\n-\t\t-normGC <target GC profile file> (i.e. tagGCcontent.txt file from control experiment)\n-\t\t\tUse "-normGC default" to match the genomic GC distribution\n-\t\t-normFixedOligo <oligoFreqFile> (normalize 5' end bias, "-normFixedOligo default" ok)\n-\t\t-minNormRatio <#> (Minimum deflation ratio of tag counts, default: 0.25)\n-\t\t-maxNormRatio <#> (Maximum inflation ratio of tag counts, default: 2.0)\n-\t\t-iterNorm <#> (Sets -max/minNormRatio to 1 and 0, iteratively normalizes such that the\n-\t\t\tresulting distrubtion is no more than #% different than target, i.e. 0.1,default: off)\n-\n-\tPaired-end/HiC options\n-\t\t-illuminaPE (when matching PE reads, assumes last character of read name is 0 or 1)\n-\t\t-removePEbg (remove paired end tags within 1.5x fragment length on same chr)\n-\t\t\t-PEbgLength <#> (remove PE reads facing on another within this distance, default: 1.5x fragLen)\n-\t\t-restrictionSite <seq> (i.e. AAGCTT for HindIII, assign data < 1.5x fragment length to sites)\n-\t\t\tMust specify genome sequence directory too. (-rsmis <#> to specify mismatches, def: 0)\n-\t\t\t-both, -one, -onlyOne, -none (Keeps reads near restriction sites, default: keep all)\n-\t\t\t-removeSelfLigation (removes reads linking same restriction fragment)\n-\t\t\t-removeRestrictionEnds (removes reads starting on a restriction fragment)\n-\t\t\t-assignMidPoint (will place reads in the middle of HindIII fragments)\n-\t\t\t-restrictionSiteLength <#> (maximum distance from restriction site, default: 1.5x fragLen)\n-\t\t-removeSpikes <size bp> <#> (remove tags from regions with > than # times\n-\t\t\tthe average tags per size bp, suggest "-removeSpikes 10000 5")\n-\n-\n- </help>\n-</tool>\n-\n'

diff -r 6f1302d12a38 -r 251442d07ef8 pos2bed.xml
--- a/pos2bed.xml Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,37 +0,0 @@
-<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.3">
-    <requirements>
-        <requirement type="package" version="4.1" >homer</requirement>
-    </requirements>
-    <description></description>
-    
-    <command>
-        pos2bed.pl $input_peak 1> $out_bed
-        2> $out_log || echo "Error running pos2bed." >&2
-    </command>
-    <inputs>
-        <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
-    </inputs>
-    <outputs>
-        
-        
-        <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            
-            
-        </test>
-    </tests>
-
-    <help>
-        .. class:: infomark
-
-        Converts: homer peak positions -(to)-> BED format
-
-        **Homer pos2bed.pl**
-
-        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
-    </help>
-</tool>
-

diff -r 6f1302d12a38 -r 251442d07ef8 tool_dependencies.xml
--- a/tool_dependencies.xml Wed Dec 19 20:09:58 2012 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,23 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="homer" version="4.1">
-    <install version="4.1">
-      <actions>
-        <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action>
-        
-        
-        <action type="move_directory_files">
-          <source_directory>./</source_directory>
-          <destination_directory>$INSTALL_DIR</destination_directory>
-        </action>
-        <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-      Installs homer
-    </readme>
-  </package>
-</tool_dependency>
-