Mercurial > repos > artbio > ngsplot
changeset 0:3ca58369469c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
| author | artbio |
|---|---|
| date | Wed, 06 Dec 2017 19:01:53 -0500 |
| parents | |
| children | 4dd92ce61a5c |
| files | bin/install.db.tables.r bin/ngsplotdb.py bin/remove.db.tables.r bin/setTableDefaults.py database/bootstrap/dbfile.tbl database/bootstrap/default.tbl database/bootstrap/gn_list.txt database/dbfile.tbl database/default.tbl database/gn_list.txt lib/coverage.r lib/genedb.r lib/parse.args.r lib/plotlib.r ngs.plot.r ngsplot.xml replot.xml.notworking runNGSplot.pl runreplot.pl |
| diffstat | 19 files changed, 6890 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/install.db.tables.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,73 @@ +#!/usr/bin/env Rscript +# Install the newly obtained DB tables into two ngs.plot system files: +# default.tbl and dbfile.tbl. + +args <- commandArgs(T) +# args <- c('/tmp/tmpLXAGXl', '/tmp/tmpUJduMe') +default.tbl <- args[1] +db.list <- args[2] + +# Genome-region default values. +anno.tbl <- read.table(default.tbl, header=TRUE, sep="\t", + blank.lines.skip=TRUE, stringsAsFactors=FALSE) +row.names(anno.tbl) <- paste(anno.tbl$Genome, anno.tbl$Region, sep=".") + +# Database table list. +anno.db.tbl <- read.table(db.list, + col.names=c("db.file", "Genome", "DB", "Region", + "FI.1", "FI.2", "FI.3"), + sep="\t", blank.lines.skip=TRUE, + stringsAsFactors=FALSE) +tss.tbl <- anno.db.tbl[anno.db.tbl$Region=="genebody", ] +tss.tbl$Region <- "tss" +tes.tbl <- anno.db.tbl[anno.db.tbl$Region=="genebody", ] +tes.tbl$Region <- "tes" +anno.db.tbl <- rbind(anno.db.tbl, tss.tbl, tes.tbl) +anno.db.tbl$URL <- NA # reserve for future use. + +# Extract further info columns. +default.fi <- anno.tbl[, c("DefaultFI1", "DefaultFI2", "DefaultFI3")] +db.fi <- anno.db.tbl[, c("FI.1", "FI.2", "FI.3")] +db.fi$tag <- paste(anno.db.tbl$Genome, anno.db.tbl$Region, sep=".") + +# DB scores. +getScore <- function(v.fi) { +# Calculate DB score based on intersection with default values. +# Args: +# v.fi: character vector of further infos. +# Returns: integer of DB score. + + default.vals <- default.fi[v.fi["tag"], ] + fi.vals <- v.fi[c("FI.1", "FI.2", "FI.3")] + 3 - length(intersect(default.vals, fi.vals)) +} +db.score <- apply(db.fi, 1, getScore) +anno.db.tbl$dbScore <- db.score + +# Save to text output. +progpath <- Sys.getenv('NGSPLOT') +if(progpath == "") { + stop("Set environment variable NGSPLOT before run the program. See README for details.\n") +} +def.f <- file.path(progpath, 'database', 'default.tbl') +db.f <- file.path(progpath, 'database', 'dbfile.tbl') +org.anno.tbl <- read.delim(def.f) +org.anno.db.tbl <- read.delim(db.f) +anno.tbl <- rbind(org.anno.tbl, anno.tbl) +anno.tbl <- unique(anno.tbl) +anno.db.tbl <- rbind(org.anno.db.tbl, anno.db.tbl) +anno.db.tbl <- unique(anno.db.tbl) +write.table(anno.tbl, file=def.f, row.names=F, sep="\t", quote=F) +write.table(anno.db.tbl, file=db.f, row.names=F, sep="\t", quote=F) + +# getScore <- function(i, db.fi, default.fi){ +# score <- 3 - length(intersect(as.matrix(default.fi[db.fi[i, "tag"], ]), as.matrix(db.fi[i, ]))) +# return(score) +# } + +# for (i in (1:dim(db.fi)[1])){ +# anno.db.tbl[i, "dbScore"] <- getScore(i, db.fi, default.fi) +# } + +# anno.version="0.01" +# save(anno.tbl, anno.db.tbl, anno.version, file="database.RData")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/ngsplotdb.py Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,670 @@ +#!/usr/bin/env python +# +# ngsplotdb - PYTHON script to manipulate the ngs.plot database installation. +# Author: Li Shen, Mount Sinai School of Medicine +# Date created: Dec 28, 2012 +# Last updated: May 28, 2013 +# +# Functions implemented: +# +# list - List locally installed genomes. +# check - Check the integrity of local database. +# install - Install a genome from ngsplotdb.XXX.tar.gz. +# remove - Remove a locally installed genome. + + +# def dir_to_idspec(dirn): +# """Convert an FTP directory name to species ID and Name. +# This works with both UCSC and Ensembl FTP. +# """ +# parts = dirn.split('_') +# sid = parts[0][:3].lower() + parts[1][:3].lower() +# spec = str.title(parts[0] + ' ' + parts[1]) +# return sid, spec + +# def listremote(database="refseq"): +# """List available genomes on a remote FTP site.""" + +# import urllib2 + +# url_ensembl = "ftp://ftp.ensembl.org/pub/current_gtf/" +# url_ucsc = "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/" + +# if database == "refseq": +# ftp = urllib2.urlopen(url_ucsc) +# elif database == "ensembl": +# ftp = urllib2.urlopen(url_ensembl) +# else: +# pass + +# # Read directory names from the remote FTP site. +# dir_names = ftp.read().splitlines() +# # Parse lines to obtain clean directory names only. +# if database == "refseq": +# dir_names = map(lambda x: x.split()[-3], dir_names) +# elif database == "ensembl": +# dir_names = map(lambda x: x.split()[-1], dir_names) +# else: +# pass +# # Filter directory names that do not correspond to a species. +# # On UCSC FTP, both "." and ".." will be retrieved from above and can +# # cause troubles. + +# id_spec_list = map(dir_to_idspec, dir_names) +# print "ID\tName" +# for r in id_spec_list: +# print r[0], "\t", r[1] + +def read_gnlist(root_path, mode): + """Read installed genomes list. + + Args: + root_path: ngs.plot installation directory. + mode: row reading mode - "vector" or "hash", correspond to each record + read as a vector of hash table. + Returns: (header split vector, hash table of installed genomes, + vector of column widths) + """ + from collections import defaultdict + + gn_list = root_path + "/database/gn_list.txt" + try: + db_f = open(gn_list, "r") + except IOError: + print "Open {0} error: your ngs.plot database may be corrupted.".\ + format(gn_list) + sys.exit() + + default_list = root_path + "/database/default.tbl" + try: + default_f = open(default_list, "r") + except IOError: + print "Open {0} error: your ngs.plot database may be corrupted.".\ + format(default_list) + sys.exit() + default_l = [] + header = default_f.readline() # skip the header + for rec in default_f: + r_sp = rec.rstrip().split("\t") + default_l.append((r_sp[0], r_sp[2])) # tuple of genome and region, like ("dm3", "genebody") + genome_region_dict = defaultdict(list) + for genome,region in default_l: + genome_region_dict[genome].append(region) + + header = db_f.readline() + h_sp = header.rstrip().split("\t") + h_sp.append("InstalledFeatures") + v_cw = map(len, h_sp) # column widths initialize to header widths. + + g_tbl = {} + for rec in db_f: + r_sp = rec.rstrip().split("\t") + r_sp.append(",".join(genome_region_dict[r_sp[0]])) + r_cw = map(len, r_sp) + v_cw = map(max, v_cw, r_cw) + + r_tbl = dict(zip(h_sp, r_sp)) + if(mode == "vector"): + g_tbl[r_tbl["ID"]] = r_sp + elif(mode == "hash"): + g_tbl[r_tbl["ID"]] = r_tbl + else: + pass + + db_f.close() + + return (h_sp, g_tbl, v_cw) + + +def update_gnlist(root_path, g_tbl, gn, assembly, species, ens_v, np_v): + """Update/Add genomes in ngs.plot database. + + Args: + root_path: ngs.plot installation directory. + g_tbl: genome hash table. Each value is also a hash table of + genome info. + gn: genome name. + assembly: genome assembly name. + species: species name. + ens_v: new Ensembl version. + np_v: new ngs.plot version. + Returns: None + """ + + if gn in g_tbl: + g_tbl[gn]["EnsVer"] = ens_v + g_tbl[gn]["NPVer"] = np_v + else: + g_tbl[gn] = {"ID": gn, "Assembly": assembly, "Species": species, \ + "EnsVer": ens_v, "NPVer": np_v} + + write_gnlist(root_path, g_tbl) + + +def write_gnlist(root_path, g_tbl): + """Write genome hash table to database file: gn_list.txt. + + Args: + root_path: ngs.plot installation directory. + g_tbl: genome hash table. Each value is also a hash table of + genome info. + Returns: None + """ + + output_order = ["ID", "Assembly", "Species", "EnsVer", "NPVer"] + gn_list = root_path + "/database/gn_list.txt" + + try: + db_f = open(gn_list, "w") + except IOError: + print "Open {0} error: your ngs.plot database may be corrupted.".\ + format(gn_list) + sys.exit() + + db_f.write("\t".join(output_order) + "\n") + + for k in g_tbl.viewkeys(): + rec = [] + for col in output_order: + rec.append(str(g_tbl[k][col])) + db_f.write("\t".join(rec) + "\n") + + db_f.close() + + +def listgn(root_path, args): + """List installed genomes in local database on screen. + + Args: + root_path: ngs.plot installation directory. + args: currently not used. + Returns: None. + """ + + import math + + (h_sp, g_tbl, v_cw) = read_gnlist(root_path, "vector") + + # Format column widths to beautify output. + tab_u = 4 + v_cw = map(lambda x: int(math.ceil(float(x) / tab_u) * tab_u + 1), v_cw) + + # List genomes to screen. + print "".join(map(lambda x, y: x.ljust(y), h_sp, v_cw)) # header. + for k in sorted(g_tbl.viewkeys(), key=str.lower): + print "".join(map(lambda x, y: x.ljust(y), g_tbl[k], v_cw)) + +def isExAnno(pkg_files): + """If the package is an extension package based on cell lines for ngs.plot, + like enhancer or dhs. + + Args: + pkg_files: list of files in the package. + Returns: + isEx: Bool, if the package is an extension package. + feature: string, feature name contained in the extension package. None + if not an extension package. + RDcount: number of RData tables in the package. + """ + + import os.path + + exclusive_files = [".chrnames.refseq", ".chrnames.ensembl", ".metainfo"] + isEx = False + RDcount = 0 + feature = None + for file_name in pkg_files: + if os.path.basename(file_name) in exclusive_files: + continue + if (not file_name.endswith("RData")) and (file_name.count("/")) > 0: + isEx = True + feature = file_name.split("/")[1] + elif file_name.endswith("RData"): + RDcount += 1 + return (isEx, feature, RDcount) + +def install(root_path, args): + """Interactive session for installing genome from package file. + + Args: + root_path: ngs.plot installation directory. + args.yes: say yes to all questions. + args.pkg: path of package file. + Returns: + None. + """ + + import tarfile + import sys + + yestoall = args.yes + pkg_file = args.pkg + # Package name: e.g. ngsplotdb_mm10_71_1.0.tar.gz. + # Information about the genome is in mm10/.metainfo. + try: + pkg_f = tarfile.open(pkg_file, "r:gz") + except tarfile.ReadError: + print "Read package file {0} error.".format(pkg_file), + print "The downloaded file may be corrupted." + sys.exit() + + print "Extracting information from package...", + sys.stdout.flush() + pkg_files = pkg_f.getnames() + g_folder = pkg_files[0] + # Minus folder name and .metainfo file name. + (isEx, feature, RDcount) = isExAnno(pkg_files) + if isEx: + print feature + " extension package, ", + print "contains " + str(RDcount + 2) + " tables." + else: + print "contains " + str(RDcount + 2) + " tables." + # .metainfo file: + # "ID"<TAB>mm10 + # "Assembly"<TAB>GRCm38 + # "Species"<TAB>mus_musculus + # "EnsVer"<TAB>71 + # "NPVer"<TAB>1.0 + meta_f = pkg_f.extractfile(g_folder + "/.metainfo") + meta_tbl = {} + if meta_f: + for rec in meta_f: + rec_sp = rec.strip().split("\t") + meta_tbl[rec_sp[0]] = rec_sp[1] # format: Variable<TAB>Value + else: + print "No meta information found in the package file.", + print "The downloaded file may be corrupted." + sys.exit() + meta_f.close() + pkg_f.close() + + gn_inst = meta_tbl["ID"] + assembly = meta_tbl["Assembly"] + species = meta_tbl["Species"] + ens_ver = float(meta_tbl["EnsVer"]) + np_ver = float(meta_tbl["NPVer"]) + + # Database file. + (h_sp, g_tbl, v_cw) = read_gnlist(root_path, "hash") + + if gn_inst in g_tbl: + installed_ens = float(g_tbl[gn_inst]["EnsVer"]) + installed_np = float(g_tbl[gn_inst]["NPVer"]) + + # For extension package. + # Only the same version with basic package could be installed. + if isEx: + if ens_ver == installed_ens and np_ver == installed_np: + print "Will upgrade the genome {0} with {1} annotation:".format(gn_inst, \ + feature), + print "Ensembl: {0}; ngs.plot: {1}.".\ + format(installed_ens, np_ver) + if yestoall: + install_pkg(root_path, pkg_file, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + else: + ans = raw_input("Continue?(y/n): ") + while True: + if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"): + break + else: + ans = raw_input("Answer must be y/Y or n/N: ") + if(ans == "y" or ans == "Y"): + install_pkg(root_path, pkg_file, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + return + else: + print "This is an extension package of " + feature + \ + ", ENS version " + str(ens_ver) + ", NPVer" + str(np_ver) + \ + ", please install the same version basic genome annotation first!" + return + + # For basic package. + # Install a newer version. + if ens_ver > installed_ens or \ + ens_ver == installed_ens and np_ver > installed_np: + print "Will upgrade the genome {0}:".format(gn_inst) + print "Ensembl: {0}==>{1}; ngs.plot: {2}==>{3}.".\ + format(installed_ens, ens_ver, installed_np, np_ver), + if yestoall: + install_pkg(root_path, pkg_file, gn_inst, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + else: + ans = raw_input("Continue?(y/n): ") + while True: + if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"): + break + else: + ans = raw_input("Answer must be y/Y or n/N: ") + if(ans == "y" or ans == "Y"): + install_pkg(root_path, pkg_file, gn_inst, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + # Install an older version. + else: + print "Will install the same or older version", + print "of the genome {0}:".format(gn_inst) + print "Ensembl: {0}==>{1}; ngs.plot: {2}==>{3}.".\ + format(installed_ens, ens_ver, installed_np, np_ver), + if yestoall: + install_pkg(root_path, pkg_file, gn_inst, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + else: + ans = raw_input("Continue?(y/n): ") + while True: + if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"): + break + else: + ans = raw_input("Answer must be y/Y or n/N: ") + if(ans == "y" or ans == "Y"): + install_pkg(root_path, pkg_file, gn_inst, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + # Totally new installation, only basic package could be installed. + else: + print "Will install new genome {0}:".format(gn_inst), + print "Ensembl=> v{0}; ngs.plot=> v{1}.".format(ens_ver, np_ver), + if yestoall: + install_pkg(root_path, pkg_file, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + else: + ans = raw_input("Continue?(y/n): ") + + while True: + if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"): + break + else: + ans = raw_input("Answer must be y/Y or n/N:") + if(ans == "y" or ans == "Y"): + install_pkg(root_path, pkg_file, gn_inst) + update_gnlist(root_path, g_tbl, gn_inst, assembly, \ + species, ens_ver, np_ver) + + +def install_pkg(root_path, pkg_file, new_gn, old_gn=None): + """Install genome from package file. + + Args: + root_path: ngs.plot installation directory. + pkg_file: package file name. + old_gn: old genome name to be removed first. + Returns: + None. + """ + + import shutil + import tarfile + import sys + + if old_gn: + print "Removing installed genome:{0}...".format(old_gn), + sys.stdout.flush() + shutil.rmtree(root_path + '/database/' + old_gn) + rm_dbtbl(root_path, old_gn) + print "Done" + + print "Installing new genome...", + sys.stdout.flush() + try: + tar_f = tarfile.open(pkg_file, "r:gz") + except tarfile.ReadError: + print "Read package file {0} error: ".format(pkg_file), + print "downloaded file may be corrupted." + sys.exit() + + try: + tar_f.extractall(root_path + "/database") + except tarfile.ExtractError: + print "Extract files from package error.", + print "The downloaded file may be corrupted." + + add_dbtbl(root_path, new_gn) + + print "Done" + + +def add_dbtbl(root_path, gn): + """Add a new genome into database meta tables. + + Args: + root_path: ngs.plot installation directory. + gn: genome name to add. + Returns: None. + """ + + import os.path + import os + import glob + import tempfile + import subprocess + + (dblist_f, dblist_n) = tempfile.mkstemp(text=True) + (gnlist_f, gnlist_n) = tempfile.mkstemp(text=True) + + # Obtain a list of .RData file names to extract info from. + all_rdata = root_path + '/database/{0}/{1}*.RData'.format(gn, gn) + all_set = set(map(os.path.basename, glob.glob(all_rdata))) + all_rdata = root_path + '/database/{0}/*/{1}*.RData'.format(gn, gn) + all_set = all_set | set(map(os.path.basename, glob.glob(all_rdata))) + exm_rdata = root_path + '/database/{0}/{1}*exonmodel*.RData'.format(gn, gn) + exm_set = set(map(os.path.basename, glob.glob(exm_rdata))) + nex_list = sorted(list(all_set - exm_set)) + + # DB file list. + gn_ens_list = {} # Ensembl genome name unique list. + desired_ncols = 6 + for fname in nex_list: + tokens = fname.split('.') + tokens = tokens[:6] + if tokens[-1] == 'RData': + tokens[-1] = 'NA' + tokens.extend(['NA'] * (desired_ncols - len(tokens))) + os.write(dblist_f, fname + "\t" + "\t".join(tokens) + "\n") + if tokens[1] == 'ensembl': + gn_ens_list[".".join(tokens[:3])] = 1 + os.close(dblist_f) + + # Ensembl genome name list. + for gn in sorted(gn_ens_list.viewkeys()): + os.write(gnlist_f, gn.replace(".", "\t") + "\n") + os.close(gnlist_f) + + # Call external program to create table default file. + (default_f, default_n) = tempfile.mkstemp(text=True) + subprocess.call(["setTableDefaults.py", gnlist_n, default_n]) + os.remove(gnlist_n) + + # Call external program to calcualte DB score and install the new entries + # into ngs.plot database. + subprocess.call(["install.db.tables.r", default_n, dblist_n]) + os.remove(default_n) + os.remove(dblist_n) + + +def remove(root_path, args): + """Remove genome from ngs.plot database. + + Args: + root_path: ngs.plot installation directory. + args.yes: say yes to all questions. + args.gn: genome name. + Returns: + None. + """ + + import shutil + import sys + + yestoall = args.yes + sub_ftr = args.ftr + + (h_sp, g_tbl, v_cw) = read_gnlist(root_path, "hash") + + gn = args.gn + + if gn in g_tbl and sub_ftr is None: + print "Will remove genome {0} from database.".format(gn), + do_rm = False + if yestoall: + do_rm = True + else: + ans = raw_input("Continue?(y/n): ") + while True: + if ans == 'y' or ans == 'Y' or ans == 'n' or ans == 'N': + break + else: + ans = raw_input("The answer must be y/Y or n/N: ") + if ans == 'y' or ans == 'Y': + do_rm = True + if do_rm: + folder_to_rm = root_path + "/database/" + gn + print "Removing genome...", + sys.stdout.flush() + shutil.rmtree(folder_to_rm) + del g_tbl[gn] + write_gnlist(root_path, g_tbl) + rm_dbtbl(root_path, gn) + print "Done" + elif gn in g_tbl and sub_ftr is not None: + print "Will remove genomic feature {0} of genome {1} from database."\ + .format(sub_ftr, gn) + do_rm = False + if yestoall: + do_rm = True + else: + ans = raw_input("Continue?(y/n): ") + while True: + if ans == 'y' or ans == 'Y' or ans == 'n' or ans == 'N': + break + else: + ans = raw_input("The answer must be y/Y or n/N: ") + if ans == 'y' or ans == 'Y': + do_rm = True + if do_rm: + folder_to_rm = root_path + "/database/" + gn + "/" + sub_ftr + print "Removing genome...", + sys.stdout.flush() + shutil.rmtree(folder_to_rm) + # g_tbl does't need to be updated + rm_dbtbl(root_path, gn, sub_ftr) + print "Done" + else: + print "Cannot find the genome in database. Nothing was done." + + +def rm_dbtbl(root_path, gn, sub_ftr=None): + """Remove a genome from database meta tables. + + Args: + root_path: ngs.plot installation directory. + gn: genome name to remove. + Returns: None. + """ + + import subprocess + + if sub_ftr is None: + subprocess.call(["remove.db.tables.r", gn]) + else: + subprocess.call(["remove.db.tables.r", gn, sub_ftr]) + +def chrnames(root_path, args): + """List chromosome names for a given genome. + + Args: + root_path: ngs.plot installation directory. + args.gn: genome name to remove. + args.db: database(ensembl or refseq). + Returns: None. + """ + + import sys + + db = args.db + gn = args.gn + + if db != "ensembl" and db != "refseq": + print "Unrecognized database name: database must be ensembl or refseq." + sys.exit() + + chrnames_file = root_path + "/database/" + gn + "/.chrnames." + db + + try: + chrf = open(chrnames_file) + except IOError: + print "Open file: {0} error.".format(chrnames_file), + print "Your database may be corrupted or you have an older version." + sys.exit() + + chr_list = chrf.read(1000000) # set 1MB limit to avoid nasty input. + chrf.close() + + chr_list = chr_list.strip() + print chr_list + + + +############################################### +######## Main procedure. ###################### +if __name__ == "__main__": + + import argparse + import os + import sys + + try: + root_path = os.environ["NGSPLOT"] + except KeyError: + print "Environmental variable NGSPLOT is not set! Exit.\n" + sys.exit() + + # Main parser. + parser = argparse.ArgumentParser(description="Manipulate ngs.plot's \ + annotation database", + prog="ngsplotdb.py") + parser.add_argument("-y", "--yes", help="Say yes to all prompted questions", + action="store_true") + + subparsers = parser.add_subparsers(title="Subcommands", + help="additional help") + + # ngsplotdb.py list parser. + parser_list = subparsers.add_parser("list", help="List genomes installed \ + in database") + parser_list.set_defaults(func=listgn) + + # ngsplotdb.py install parser. + parser_install = subparsers.add_parser("install", + help="Install genome from package \ + file") + parser_install.add_argument("pkg", help="Package file(.tar.gz) to install", + type=str) + parser_install.set_defaults(func=install) + + # ngsplotdb.py remove parser. + parser_remove = subparsers.add_parser("remove", + help="Remove genome from database") + parser_remove.add_argument("gn", help="Name of genome to be \ + removed(e.g. hg18)", type=str) + parser_remove.add_argument("--ftr", help="Remove cellline specific features \ + (enhancer, dhs, etc)", type=str,\ + default=None) + parser_remove.set_defaults(func=remove) + + # ngsplotdb.py chromosome names parser. + parser_chrnames = subparsers.add_parser("chrnames", + help="List chromosome names") + parser_chrnames.add_argument("gn", help="Genome name(e.g. mm9)", type=str) + parser_chrnames.add_argument("db", help="Database(ensembl or refseq)", + type=str) + parser_chrnames.set_defaults(func=chrnames) + + + args = parser.parse_args() + args.func(root_path, args) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/remove.db.tables.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,46 @@ +#!/usr/bin/env Rscript +# Remove the genome entries from two ngs.plot system files: +# default.tbl and dbfile.tbl. + +args <- commandArgs(T) +if(length(args)>1){ + gname.to.rm <- args[1] + feature.to.rm <- args[2] +}else{ + gname.to.rm <- args[1] +} + +# Save to text output. +progpath <- Sys.getenv('NGSPLOT') +if(progpath == "") { + stop("Set environment variable NGSPLOT before run the program. See README for details.\n") +} +default.file <- file.path(progpath, 'database', 'default.tbl') +dbfile.file <- file.path(progpath, 'database', 'dbfile.tbl') +default.tbl <- read.delim(default.file) +dbfile.tbl <- read.delim(dbfile.file) + +if(exists("feature.to.rm")){ + default.tbl <- subset(default.tbl, !(Genome==gname.to.rm & Region==feature.to.rm)) + dbfile.tbl <- subset(dbfile.tbl, !(Genome==gname.to.rm & Region==feature.to.rm)) +}else{ + default.tbl <- default.tbl[default.tbl$Genome != gname.to.rm, ] + dbfile.tbl <- dbfile.tbl[dbfile.tbl$Genome != gname.to.rm, ] +} + + +write.table(default.tbl, file=default.file, row.names=F, sep="\t", quote=F) +write.table(dbfile.tbl, file=dbfile.file, row.names=F, sep="\t", quote=F) + + +# getScore <- function(i, db.fi, default.fi){ +# score <- 3 - length(intersect(as.matrix(default.fi[db.fi[i, "tag"], ]), as.matrix(db.fi[i, ]))) +# return(score) +# } + +# for (i in (1:dim(db.fi)[1])){ +# anno.db.tbl[i, "dbScore"] <- getScore(i, db.fi, default.fi) +# } + +# anno.version="0.01" +# save(anno.tbl, anno.db.tbl, anno.version, file="database.RData")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/setTableDefaults.py Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,91 @@ +#!/usr/bin/env python + +import sys +import string + +flankDict = { + "tss":2000, + "tes":2000, + "genebody":2000, + "exon":500, + "cgi":500, + "enhancer":1500, + "dhs":1000, +} + +pointLabDict = { + "tss":"TSS", + "tes":"TES", + "genebody":"TSS,TES", + "exon":"Acceptor,Donor", + "cgi":"Left,Right", + "enhancer":"Enhancer", + "dhs":"Left,Right", +} + +# FItype = { +# "tss":"endsite", +# "tes":"endsite", +# "genebody":"datatype", +# "exon":"subregion", +# "cgi":"subregion", +# "enhancer":"subregion", +# "dhs":"subregion" +# } + +in_f = file(sys.argv[1]) +out_f = file(sys.argv[2], "w") +out_f.write("\t".join(["Genome", "DefaultDB", "Region", "DefaultFI1", \ + "DefaultFI2", "DefaultFI3", "PointLab", "Flank"]) + \ + "\n") + +# while(True): +for line in in_f: + # line = in_f.readline() + # if len(line) == 0: + # break; + # line = string.strip(line) + + lineL = line.rstrip().split("\t") + genome = lineL[0] + defaultDB = lineL[1] + region = lineL[2] + + if region == "cgi": + fi_1 = "NA" + fi_2 = "ProximalPromoter" + fi_3 = "protein_coding" + elif region == "dhs": + fi_1 = "H1hesc" + fi_2 = "ProximalPromoter" + fi_3 = "protein_coding" + elif region == "exon": + fi_1 = "chipseq" + fi_2 = "canonical" + fi_3 = "protein_coding" + elif region == "genebody": + fi_1 = "chipseq" + fi_2 = "NA" + fi_3 = "protein_coding" + elif (region == "enhancer") and (genome == "hg19"): + fi_1 = "H1hesc" + fi_2 = "genebody" + fi_3 = "protein_coding" + elif (region == "enhancer") and (genome == "mm9"): + fi_1 = "mESC" + fi_2 = "genebody" + fi_3 = "protein_coding" + out_f.write("\t".join([genome, defaultDB, region, fi_1, fi_2, fi_3, \ + pointLabDict[region], str(flankDict[region])]) + "\n") + + # Extra: TSS and TES if region = genebody. + if region == "genebody": + region = "tss" + out_f.write("\t".join([genome, defaultDB, region, fi_1, fi_2, fi_3, \ + pointLabDict[region], str(flankDict[region])]) + "\n") + region = "tes" + out_f.write("\t".join([genome, defaultDB, region, fi_1, fi_2, fi_3, \ + pointLabDict[region], str(flankDict[region])]) + "\n") + +in_f.close() +out_f.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/database/bootstrap/dbfile.tbl Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,1 @@ +db.file Genome DB Region FI.1 FI.2 FI.3 URL dbScore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/database/bootstrap/default.tbl Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,1 @@ +Genome DefaultDB Region DefaultFI1 DefaultFI2 DefaultFI3 PointLab Flank
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/database/bootstrap/gn_list.txt Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,1 @@ +ID Assembly Species EnsVer NPVer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/database/dbfile.tbl Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,1 @@ +db.file Genome DB Region FI.1 FI.2 FI.3 URL dbScore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/database/default.tbl Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,1 @@ +Genome DefaultDB Region DefaultFI1 DefaultFI2 DefaultFI3 PointLab Flank
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/database/gn_list.txt Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,1 @@ +ID Assembly Species EnsVer NPVer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/coverage.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,701 @@ +# Function to check if the range exceeds coverage vector boundaries. +checkBound <- function(start, end, range, chrlen){ + if(end + range > chrlen || start - range < 1) + return(FALSE) # out of boundary. + else + return(TRUE) +} + +Bin <- function(v, n) { +# Function to bin a coverage vector. +# Args: +# v: coverage vector. +# n: number of bins. +# Return: vector of binned values. + + bin.bound <- seq(1, length(v), length.out=n + 1) + sapply(1:n, function(i) { + mean(v[bin.bound[i]:bin.bound[i + 1]]) + }) +} + +SplineRev3Sec <- function(cov.list, v.fls, pts.list, v.strand, algo="spline") { +# For 3 sections of continuous coverage, spline each according to specified +# data points and return concatenated, interpolated curves. +# Args: +# cov.list: a list of coverage vectors. Each vector represents a gene. +# v.fls: vector of flanking region size. +# pts.list: a list of three integers for data points. +# v.strand: factor vector of strands. +# algo: algorithm used to normalize coverage vectors (spline, bin). +# Return: matrix of interpolated coverage: each row represents a gene; each +# column represents a data point. Coverage from exons are concatenated. +# Notes: the names of cov.list and pts.list must be the same for index purpose. +# Suggested: use 'l', 'm', and 'r' for the names. + + # Create an empty coveage matrix first. + tot.pts <- sum(unlist(pts.list)) - 2 + cov.mat <- matrix(nrow=length(cov.list), ncol=tot.pts) + + for(i in 1:length(cov.list)) { + left.cov <- head(cov.list[[i]], n=v.fls[i]) + right.cov <- tail(cov.list[[i]], n=v.fls[i]) + mid.cov <- window(cov.list[[i]], start=v.fls[i] + 1, + width=length(cov.list[[i]]) - 2*v.fls[i]) + if(algo == "spline") { + left.cov <- spline(1:length(left.cov), left.cov, n=pts.list$l)$y + right.cov <- spline(1:length(right.cov), right.cov, n=pts.list$r)$y + mid.cov <- spline(1:length(mid.cov), mid.cov, n=pts.list$m)$y + } else if(algo == "bin") { + left.cov <- Bin(left.cov, n=pts.list$l) + right.cov <- Bin(right.cov, n=pts.list$r) + mid.cov <- Bin(mid.cov, n=pts.list$m) + } else { + # pass. + } + # Fuse the two points at the boundary and concatenate. + f1 <- (tail(left.cov, n=1) + head(mid.cov, n=1)) / 2 + f2 <- (tail(mid.cov, n=1) + head(right.cov, n=1)) / 2 + con.cov <- c(left.cov[-length(left.cov)], f1, + mid.cov[-c(1, length(mid.cov))], + f2, right.cov[-1]) + # browser() + if(v.strand[i] == '+') { + cov.mat[i, ] <- con.cov + } else { + cov.mat[i, ] <- rev(con.cov) + } + } + + cov.mat +} + +extrCov3Sec <- function(v.chrom, v.start, v.end, v.fls, v.strand, m.pts, f.pts, + bufsize, algo, ...) { +# Extract and interpolate coverage vectors from genomic regions with 3 sections. +# Args: +# v.chrom: factor vector of chromosome names. +# v.start: integer vector of region start. +# v.end: integer vector of region end. +# v.fls: integer vector of flanking region size in bps. +# v.strand: factor vector of gene strands. +# m.pts: data points for middle interval. +# f.pts: data points for flanking region. +# bufsize: integer; buffers are added to both ends of each region. +# algo: algorithm used to normalize coverage vectors. +# Return: matrix of interpolated coverage: each row represents a gene; each +# column represents a data point. + + interflank.gr <- GRanges(seqnames=v.chrom, ranges=IRanges( + start=v.start - v.fls - bufsize, + end=v.end + v.fls + bufsize)) + interflank.cov <- covBamExons(interflank.gr, v.strand, ...) + + # Trim buffers from coverage vectors. + interflank.cov <- lapply(interflank.cov, function(v) { + window(v, start=bufsize + 1, width=length(v) - 2 * bufsize) + }) + + # Interpolate and reverse coverage vectors. + SplineRev3Sec(interflank.cov, v.fls, list(l=f.pts, m=m.pts, r=f.pts), + v.strand, algo) +} + +sub3CovList <- function(all.cov, v.left, v.right) { +# For a list of coverage vectors, separate them into three lists. +# Args: +# all.cov: list of coverage vectors. +# v.left: integer vector of left flanking size. +# v.right: integer vector of right flanking size. +# Return: list of lists of coverage vectors. The outer list is named as: +# "l", "m", "r". + + left.cov <- foreach(i=icount(length(all.cov))) %do% { + head(all.cov[[i]], n=v.left[i]) + } + mid.cov <- foreach(i=icount(length(all.cov))) %do% { + len <- length(all.cov[[i]]) + all.cov[[i]][ (v.left[i] + 1) : (len - v.right[i]) ] + } + right.cov <- foreach(i=icount(length(all.cov))) %do% { + tail(all.cov[[i]], n=v.right[i]) + } + list(l=left.cov, m=mid.cov, r=right.cov) +} + +extrCovExons <- function(v.chrom, exonranges.list, v.fls, v.strand, + m.pts, f.pts, bufsize, algo, ...) { +# Extract coverage vectors for transcripts with exon models. +# Args: +# v.chrom: factor vector of chromosome names. +# exonranges.list: list of IRanges objects for exon coordinates. +# v.fls: integer vector of flanking region size in bps. +# v.strand: factor vector of gene strands. +# m.pts: data points for middle interval. +# f.pts: data points for flanking region. +# bufsize: integer; buffers are added to both ends of each region. +# algo: algorithm used to normalize coverage vectors. +# Return: matrix of interpolated coverage: each row represents a gene; each +# column represents a data point. Coverage from exons are concatenated. + + # Construct ranges including exon and flanking regions. + exonflank.list <- vector('list', length=length(exonranges.list)) + for(i in 1:length(exonranges.list)) { + r.mod <- exonranges.list[[i]] # IRanges object to be modified. + n <- length(r.mod) + # Add flanking and buffer regions. + start(r.mod)[1] <- start(r.mod)[1] - v.fls[i] - bufsize + end(r.mod)[n] <- end(r.mod)[n] + v.fls[i] + bufsize + exonflank.list[[i]] <- GRanges(seqnames=v.chrom[i], ranges=r.mod) + } + + exonflank.cov <- covBamExons(exonflank.list, v.strand, ...) + + # Trim buffers from coverage vectors. + exonflank.cov <- lapply(exonflank.cov, function(v) { + window(v, start=bufsize + 1, width=length(v) - 2 * bufsize) + }) + + SplineRev3Sec(exonflank.cov, v.fls, list(l=f.pts, m=m.pts, r=f.pts), + v.strand, algo) +} + + +extrCovMidp <- function(v.chrom, v.midp, flanksize, v.strand, pts, bufsize, + algo, ...) { +# Extract coverage vectors with a middle point and symmetric flanking regions. +# Args: +# v.chrom: factor vector of chromosome names. +# v.midp: integer vector of middle points. +# flanksize: integer of flanking region size in bps. +# v.strand: factor vector of gene strands. +# pts: data points to spline into. +# bufsize: integer; buffers are added to both ends of each region. +# algo: algorithm used to normalize coverage vectors. +# Return: matrix of interpolated coverage: each row represents a gene; each +# column represents a data point. + + granges <- GRanges(seqnames=v.chrom, ranges=IRanges( + start=v.midp - flanksize - bufsize, + end=v.midp + flanksize + bufsize)) + cov.list <- covBamExons(granges, v.strand, ...) + + # Trim buffers from coverage vectors. + cov.list <- lapply(cov.list, function(v) { + window(v, start=bufsize + 1, width=length(v) - 2 * bufsize) + }) + + # Interpolate and reverse coverage vectors and assemble into a matrix. + cov.mat <- matrix(nrow=length(cov.list), ncol=pts) + for(i in 1:length(cov.list)) { + if(is.null(cov.list[[i]])) { + cov.mat[i, ] <- vector('integer', length=pts) + } else { + if(algo == "spline") { + cov.mat[i, ] <- spline(1:length(cov.list[[i]]), cov.list[[i]], + n=pts)$y + } else if(algo == "bin") { + cov.mat[i, ] <- Bin(cov.list[[i]], n=pts) + } else { + # pass. + } + if(v.strand[i] == '-') { + cov.mat[i, ] <- rev(cov.mat[i, ]) + } + } + } + cov.mat +} + +scanBamRevOrder <- function(org.gr, sbp) { +# ScanBamParam re-arranges the input genomic ranges. Use range info to +# construct a string vector to find the order to reverse it. + org.grnames <- with(org.gr, paste(seqnames, start, end, sep=':')) + sbw.gr <- as.data.frame(bamWhich(sbp)) # scan-bam-ed + if('space' %in% names(sbw.gr)) { + sbw.grnames <- with(sbw.gr, paste(space, start, end, sep=':')) + } else if('group_name' %in% names(sbw.gr)) { + sbw.grnames <- with(sbw.gr, paste(group_name, start, end, sep=':')) + } else { + stop("Cannot locate chromosome names in extracted short reads. Report +this problem using issue tracking or discussion forum.\n") + } + + match(org.grnames, sbw.grnames) +} + +genZeroList <- function(llen, v.vlen) { +# Generate a list of specific length with each element being an Rle vector of +# zeros with specific length. +# Args: +# llen: list length +# v.vlen: vector of vector lengths. + + llen <- as.integer(llen) + stopifnot(llen > 0) + res <- vector('list', length=llen) + for(i in 1:llen) { + res[[i]] <- Rle(0, v.vlen[i]) + } + res +} + +covBamExons <- function(granges.dat, v.strand, bam.file, sn.inbam, fraglen, + map.qual=20, bowtie=F, + strand.spec=c('both', 'same', 'opposite')) { +# Extract coverage vectors from bam file for a list of transcripts of multiple +# exons. +# Args: +# granges.dat: a GRanges object representing a set of genomic ranges or a +# list of GRanges objects each representing a set of exonic +# ranges. +# v.strand: vector of strand info. +# bam.file: character string refers to the path of a bam file. +# sn.inbam: vector of chromosome names in the bam file. +# fraglen: fragment length. +# map.qual: mapping quality to filter reads. +# bowtie: boolean to indicate whether the aligner was Bowtie-like or not. +# strand.spec: string desc. for strand-specific coverage calculation. +# Return: list of coverage vectors, each vector represents a transcript. + + strand.spec <- match.arg(strand.spec) + + if(class(granges.dat) == 'list') { + # Construct a GRanges object representing DNA sequences. + v.seqnames <- sapply(granges.dat, + function(x) as.character(seqnames(x)[1])) + v.start <- sapply(granges.dat, function(x) start(ranges(x))[1]) + v.end <- sapply(granges.dat, function(x) tail(end(ranges(x)), n=1)) + granges.dna <- GRanges(seqnames=v.seqnames, + ranges=IRanges(start=v.start, end=v.end)) + # Obtain mRNA(including flanking) length for each gene. + repr.lens <- sapply(granges.dat, function(g) { + sum(end(g) - start(g) + 1) + }) + } else { + v.seqnames <- as.character(seqnames(granges.dat)) + v.start <- start(granges.dat) + v.end <- end(granges.dat) + granges.dna <- granges.dat + repr.lens <- v.end - v.start + 1 + granges.dat <- vector('list', length(granges.dna)) # set null tags. + } + + # Filter transcripts whose chromosomes do not match bam file. + inbam.mask <- as.character(seqnames(granges.dna)) %in% sn.inbam + if(!any(inbam.mask)) { # none matches. + return(genZeroList(length(granges.dna), repr.lens)) + } + + # scanBamWhat: the info that need to be extracted from a bam file. + sbw <- c('pos', 'qwidth', 'mapq', 'strand', 'rname', + 'mrnm', 'mpos', 'isize') + sbp <- ScanBamParam(what=sbw, which=granges.dna[inbam.mask], + flag=scanBamFlag(isUnmappedQuery=F, + isNotPassingQualityControls=F, + isDuplicate=F)) + + # Scan bam file to retrieve short reads. + sr.in.ranges <- tryCatch(scanBam(bam.file, param=sbp), error=function(e) e) + if(class(sr.in.ranges)[1] == 'simpleError') { + # This is not supposed to happen after those unmatched seqnames are + # removed. I keep it for safty. + return(genZeroList(length(granges.dna), repr.lens)) + } + + # Restore the original order. + sr.in.ranges <- sr.in.ranges[scanBamRevOrder( + as.data.frame(granges.dna[inbam.mask]), sbp)] + + CalcReadsCov <- function(srg, start, end, gr.rna, repr.len, strand) { + # Calculate short read coverage for each gene/region. + # Args: + # srg: extracted short reads in gene. + # start: start position of the DNA sequence. + # end: end position of the DNA sequence. + # gr.rna: GRanges object (multiple ranges) representing exon sequences. + # This can be NULL indicating the input ranges are DNAs. + # repr.len: DNA or mRNA sequence length. + # strand: transcript strand (+/-). + # Returns: a coverage vector for the gene. + + # browser() + # Special handling for bowtie mapping. + if(bowtie) { + srg <- within(srg, mapq[is.na(mapq)] <- 254) # within! + } + # Filter short reads by mapping quality. + all.mask <- srg$mapq >= map.qual + + # Subset by strand info. + if(strand.spec != 'both') { + if(strand.spec == 'same') { + s.mask <- srg$strand == as.character(strand) + } else { + s.mask <- srg$strand != as.character(strand) + } + all.mask <- all.mask & s.mask + } + + # If paired, filter reads that are not properly paired. + paired <- all(with(srg, is.na(isize) | isize != 0)) + if(paired) { + p.mask <- with(srg, rname == mrnm & xor(strand == '+', isize < 0)) + all.mask <- all.mask & p.mask + } + + # Apply all the filters on short reads. + srg <- lapply(srg, `[`, which(all.mask)) + + # Calculate coverage. + if(length(srg[[1]]) > 0) { + if(paired) { + cov.pos <- with(srg, ifelse(isize < 0, mpos, pos)) + cov.wd <- abs(srg$isize) + } else { + # Adjust negative read positions for physical coverage. + cov.pos <- with(srg, ifelse(strand == '-', + pos - fraglen + qwidth, pos)) + cov.wd <- fraglen + } + # Shift reads by subtracting start positions. + cov.pos <- cov.pos - start + 1 + # Calculate physical coverage on the whole genebody. + covg <- coverage(IRanges(start=cov.pos, width=cov.wd), + width=end - start + 1, method='sort') + + if(!is.null(gr.rna)) { # RNA-seq. + # Shift exonic ranges by subtracting start positions. + # BE careful with negative start positions! Need to adjust end + # positions first(or the GRanges lib will emit errors if + # start > end). + # Negative start positions happen when flanking region exceeds + # the chromosomal start. + if(start > 0) { + start(gr.rna) <- start(gr.rna) - start + 1 + end(gr.rna) <- end(gr.rna) - start + 1 + } else { + end(gr.rna) <- end(gr.rna) - start + 1 + start(gr.rna) <- start(gr.rna) - start + 1 + } + # Concatenate all exon coverages. + covg[ranges(gr.rna)] + } else { # ChIP-seq. + covg + } + } else { + Rle(0, repr.len) + } + } + + covg.allgenes <- mapply(CalcReadsCov, srg=sr.in.ranges, + start=v.start, end=v.end, gr.rna=granges.dat, + repr.len=repr.lens, strand=v.strand, SIMPLIFY=F) +} + +bamFileList <- function(ctg.tbl) { +# Determine the bam files involved in the configuration and whether it is a +# bam file pair setup. +# Args: +# ctg.tbl: coverage-genelist-title table. + + cov.uniq <- unique(ctg.tbl$cov) + cov.list <- strsplit(cov.uniq, ':') + v.nbam <- sapply(cov.list, length) + v.bbp <- v.nbam == 2 + if(all(v.bbp)) { + bbp <- T + } else if(all(!v.bbp)) { + bbp <- F + } else { + stop("No mix of bam and bam-pair allowed in configuration.\n") + } + + list(bbp=bbp, bam.list=unique(unlist(cov.list))) +} + +estiMapqStyle <- function(bam.file){ +# Estimate the mapping quality style. Return TRUE if it is SAM standard. +# Sample 1000 mapped reads from bam file, and if the mapq of reads +# over half are NA, then return FALSE, because it is quite possible that +# the aligner using coding style as bowtie, 255 as highest score. +# Args: +# bam.file: bam file to be sampled. + + sbw <- c('pos', 'qwidth', 'mapq', 'strand') + sbp <- ScanBamParam(what=sbw, flag=scanBamFlag( + isUnmappedQuery=F, isDuplicate=F)) + samp <- BamSampler(bam.file, yieldSize=500) + samp.reads <- scanBam(samp, param=sbp)[[1]] + samp.len <- length(samp.reads[["mapq"]]) + mapq.255 <- sum(is.na(samp.reads[["mapq"]])) + if(mapq.255/samp.len >= 0.5){ + return(FALSE) + }else{ + return(TRUE) + } +} + +headerIndexBam <- function(bam.list) { +# Read bam header to determine mapping method. +# Index bam files if not done yet. +# Args: +# ctg.tbl: coverage-genelist-title table. + + v.map.bowtie <- vector('logical', length=length(bam.list)) + for(i in 1:length(bam.list)) { + bam.file <- bam.list[i] + + # Index bam file. + if(!file.exists(paste(bam.file, ".bai", sep=""))) { + indexBam(bam.file) + } + + # Derive mapping program. + header <- scanBamHeader(bam.file) + map.prog <- try(strsplit(header[[1]]$text$'@PG'[[1]], ':')[[1]][2], + silent=T) + if(class(map.prog) != "try-error") { + map.style <- grepl('tophat|bowtie|bedtools|star', map.prog, + ignore.case=T) + if(map.style){ + v.map.bowtie[i] <- TRUE + next + } + map.style <- grepl('bwa|casava|gem', map.prog, ignore.case=T) + if(map.style) { + v.map.bowtie[i] <- FALSE + next + } +# if(estiMapqStyle(bam.file)){ +# warning(sprintf("Aligner for: %s cannot be determined. Style of +# standard SAM mapping score will be used.", bam.file)) +# v.map.bowtie[i] <- FALSE +# }else{ +# warning(sprintf("Aligner for: %s cannot be determined. Style of +# Bowtie-like SAM mapping score will be used. Would you mind to tell us what +# aligner you are using?", bam.file)) +# v.map.bowtie[i] <- TRUE +# } + } +# else { +# cat("\n") +# if(estiMapqStyle(bam.file)){ +# warning(sprintf("Aligner for: %s cannot be determined. Style of +# standard SAM mapping score will be used.", bam.file)) +# v.map.bowtie[i] <- FALSE +# }else{ +# warning(sprintf("Aligner for: %s cannot be determined. Style of +# Bowtie-like SAM mapping score will be used.", bam.file)) +# v.map.bowtie[i] <- TRUE +# } +# } + warning(sprintf("Aligner for: %s cannot be determined. Style of +standard SAM mapping score will be used. Would you mind submitting an issue +report to us on Github? This will benefit people using the same aligner.", + bam.file)) + v.map.bowtie[i] <- FALSE + } + names(v.map.bowtie) <- bam.list + + v.map.bowtie +} + +libSizeBam <- function(bam.list) { +# Obtain library sizes by counting qualified bam records. +# Args: +# ctg.tbl: coverage-genelist-title table. + + # Count only reads that are mapped, primary, passed quality control and + # un-duplicated. + sbp <- ScanBamParam(flag=scanBamFlag(isUnmappedQuery=F, isSecondaryAlignment=F, + isNotPassingQualityControls=F, isDuplicate=F)) + v.lib.size <- vector('integer', length=length(bam.list)) + for(i in 1:length(bam.list)) { + bfn <- bam.list[i] # bam file name. + cfn <- paste(basename(bfn), '.cnt', sep='') # count file name. + if(file.exists(cfn)) { + v.lib.size[i] <- as.integer(readLines(cfn, n=1)) + } else { + cnt.bam <- countBam(bfn, param=sbp) + v.lib.size[i] <- cnt.bam$records + writeLines(as.character(v.lib.size[i]), cfn) + } + names(v.lib.size)[i] <- bfn + } + + v.lib.size +} + +seqnamesBam <- function(bam.list) { +# Obtain chromosome names for each bam file. This list must be used to filter +# genomic regions before scanBam or it terminates immaturely. +# ctg.tbl: coverage-genelist-title table. + + # browser() + sn.list <- lapply(scanBamHeader(bam.list), function(h) { + names(h$targets) + }) + names(sn.list) <- bam.list + + sn.list +} + +chrTag <- function(sn.inbam) { +# Check whether the chromosome name format in the bam file contains 'chr' or not. +# Args: +# sn.inbam: seqnames in the bam file. + + n.chr <- length(grep('^chr', sn.inbam)) + if(n.chr == 0) { + chr.tag <- F + } else if(n.chr == length(sn.inbam)) { + chr.tag <- T + } else { + return("Inconsistent chromosome names in bam file. Check bam header.") + } + + chr.tag +} + +chunkIndex <- function(tot.gene, gcs) { +# Create chunk indices according to total number of genes and chunk size. +# Args: +# tot.gene: total number of genes. +# gcs: gene chunk size. + + nchk <- ceiling(tot.gene / gcs) # number of chunks. + chkidx.list <- vector('list', length=nchk) # chunk indices list. + chk.start <- 1 # chunk start. + i.chk <- idiv(tot.gene, chunkSize=gcs) + for(i in 1:nchk) { + chk.size <- nextElem(i.chk) + chkidx.list[[i]] <- c(chk.start, chk.start + chk.size - 1) + chk.start <- chk.start + chk.size + } + + chkidx.list +} + +covMatrix <- function(debug, chkidx.list, coord, rnaseq.gb, exonmodel, libsize, + spit.dot=T, ...) { +# Function to generate a coverage matrix for all genes. +# Args: +# debug: boolean tag for debugging. +# chkidx.list: list of (start, end) indices for each chunk. +# coord: dataframe of gene coordinates. +# rnaseq.gb: boolean for RNA-seq genebody plot. +# exonmodel: exon model data object. +# libsize: total read count for this bam file. +# spit.dot: boolean to control sptting '.' to consoles. +# Return: normalized coverage matrix for all genes, each row represents a gene. + + + if(!debug) { + # Extract coverage and combine into a matrix. + result.matrix <- foreach(chk=chkidx.list, .combine='rbind', + .multicombine=T) %dopar% { + if(spit.dot) { + cat(".") + } + i <- chk[1]:chk[2] # chunk: start -> end + # If RNA-seq, retrieve exon ranges. + if(rnaseq.gb) { + exonranges.list <- unlist(exonmodel[coord[i, ]$tid]) + } else { + exonranges.list <- NULL + } + doCov(coord[i, ], exonranges.list, ...) + } + + # Floor negative values which are caused by spline. + result.matrix[result.matrix < 0] <- 0 + result.matrix / libsize * 1e6 # normalize to RPM. + + } else { + for(c in 1:length(chkidx.list)) { + chk <- chkidx.list[[c]] + i <- chk[1]:chk[2] # chunk: start -> end + cat(".") + # If RNA-seq, retrieve exon ranges. + if(rnaseq.gb) { + exonranges.list <- unlist(exonmodel[coord[i, ]$tid]) + } else { + exonranges.list <- NULL + } + cov <- doCov(coord[i, ], exonranges.list, ...) + if(c == 1) { + result.matrix <- matrix(0, nrow=nrow(coord), ncol=ncol(cov)) + } + result.matrix[i, ] <- cov + } + # Floor negative values which are caused by spline. + # browser() + result.matrix[result.matrix < 0] <- 0 + result.matrix / libsize * 1e6 # normalize to RPM. + + } +} + + +doCov <- function(coord.mat, exonranges.list, chr.tag, pint, reg2plot, + flanksize, flankfactor, m.pts, f.pts, ...) { +# Extract coverage from bam file into a matrix. According to the parameter +# values, call corresponding functions. +# Args: +# coord.mat: matrix of genomic coordinates to extract coverage. +# exonranges.list: list of IRanges objects, each represents a group of exons. +# pint: boolean of point interval. +# reg2plot: string of region to plot. +# flanksize: flanking region size. +# flankfactor: flanking region factor. +# m.pts: data points for middle interval. +# f.pts: data points for flanking region. +# Return: matrix of interpolated coverage: each row represents a gene; each +# column represents a data point. Coverage from exons are concatenated. + + v.chrom <- coord.mat$chrom + # if(!chr.tag) { + # v.chrom <- sub('chr', '', v.chrom) + # } + v.chrom <- as.factor(v.chrom) + v.strand <- as.factor(coord.mat$strand) + + # Figure out interval region sizes and calculate flanking region sizes. + if(!pint) { # interval regions. + if(!is.null(exonranges.list)) { # RNA-seq + if(flankfactor > 0) { + v.fls <- sapply(exonranges.list, function(t) { + sum(end(t) - start(t) + 1) * flankfactor + }) + } else { + v.fls <- rep(flanksize, length=nrow(coord.mat)) + } + extrCovExons(v.chrom, exonranges.list, v.fls, v.strand, + m.pts, f.pts, ...) + } else { # ChIP-seq with intervals. + v.start <- coord.mat$start + v.end <- coord.mat$end + if(flankfactor > 0) { + v.fls <- round((v.end - v.start + 1) * flankfactor) + } else { + v.fls <- rep(flanksize, length=nrow(coord.mat)) + } + extrCov3Sec(v.chrom, v.start, v.end, v.fls, v.strand, + m.pts, f.pts, ...) + } + } else { # point center with flanking regions. + v.midp <- vector('integer', length=nrow(coord.mat)) + for(r in 1:nrow(coord.mat)) { + if(reg2plot == 'tss' && v.strand[r] == '+' || + reg2plot == 'tes' && v.strand[r] == '-') { + # the left site is center. + v.midp[r] <- coord.mat$start[r] + } else { # this also includes BED supplied point center. + v.midp[r] <- coord.mat$end[r] + } + } + # browser() + extrCovMidp(v.chrom, v.midp, flanksize, v.strand, m.pts + f.pts*2, ...) + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/genedb.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,258 @@ +chromFormat <- function(crn, ...){ +# Format chromosome names to our standard. +# Args: +# crn: character vector of chromosome names. +# Returns: character vector of formatted chromosome names. + + crn <- sub('.fa$', '', crn) + nochr.i <- grep('^chr', crn, invert=T) + crn[nochr.i] <- paste('chr', crn[nochr.i], sep='') + crn +} + +FIScoreIntersect <- function(db.info, v.finfo){ +# Further info score based on intersection with database FI columns. +# Used to select database files. +# Args: +# db.info: one record of annotation database table. +# v.finfo: further info that is split into vector. +# Returns: a score for the intersection between database and further info. + + length(intersect(as.vector(db.info[c("FI.1", "FI.2", "FI.3")]), v.finfo)) +} + +SetupPlotCoord <- function(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, + progpath, genome, reg2plot, lgint, flanksize, + samprate, galaxy) { +# Load genomic coordinates for plot based on the input arguments. +# Args: +# args.tbl: input argument table +# ctg.tbl: coverage-genelist-title table +# default.tbl: default settings of databases and plot setting +# dbfile.tbl: details of database files(.RData). +# progpath: program path derived from NGSPLOT +# genome: genome name, such as mm9, hg19. +# reg2plot: tss, tes, genebody, etc. +# lgint: boolean tag for large interval. +# flanksize: flanking region size. +# samprate: sampling rate +# galaxy: boolean tag for galaxy installation. + + if(reg2plot!='bed'){ + # Subset using genome-region combination. + key <- default.tbl$Genome == genome & default.tbl$Region == reg2plot + if(sum(key) == 0) { + stop("The combination of genome and region does not exist. You + may need to install the genome or the region does not exist yet.\n") + } + anno.parameters <- default.tbl[key, ] + db.match.mask <- dbfile.tbl$Genome == genome & + dbfile.tbl$Region == reg2plot + anno.db.candidates <- dbfile.tbl[db.match.mask, ] + + # Database flavor. + if('-D' %in% names(args.tbl)){ + database <- as.character(args.tbl['-D']) + database.allowed <- unique(anno.db.candidates$DB) + stopifnot(database %in% database.allowed) + }else{ + database <- as.character(anno.parameters$DefaultDB) + } + + anno.db.candidates <- anno.db.candidates[anno.db.candidates$DB == database, ] + + if (file.exists(file.path(progpath, 'database', genome, reg2plot))){ + prefix <- file.path(progpath, 'database', genome, reg2plot) + }else{ + prefix <- file.path(progpath, 'database', genome) + } + + # Further info to subset genomic regions. + if('-F' %in% names(args.tbl)){ + finfo <- as.character(args.tbl['-F']) + } else { + finfo <- NULL + } + + Labs <- unlist(strsplit(as.character(anno.parameters$PointLab[1]), ",")) + if(length(Labs)==1){ + pint <- TRUE + }else{ + pint <- FALSE + } + + if(!is.null(finfo)){ # use finfo to subset DB tables. + v.finfo <- unlist(strsplit(finfo, ',')) + # Get the intersect of the v.finfo and FI columns of databases, + # and choose the best fit. + fi.score <- apply(anno.db.candidates, 1, FIScoreIntersect, + v.finfo=v.finfo) + anno.db.candidates <- anno.db.candidates[fi.score == max(fi.score), ] + # RNA-seq tag. + if(reg2plot == 'genebody' && 'rnaseq' %in% v.finfo) { + rnaseq.gb <- TRUE + }else{ + rnaseq.gb <- FALSE + } + } else { + rnaseq.gb <- FALSE + } + anno.db.candidates <- anno.db.candidates[order(anno.db.candidates$dbScore), ] + f.load <- file.path(prefix, anno.db.candidates$"db.file"[1]) + + if (!file.exists(f.load)){ + stop("The requested database file does not exist. You may have a +corrupted database. Consider reinstalling the genome.\n") + # cat("\nDownloading database:\n") + # download.file(anno.db.candidates$"URL"[1], destfile=f.load, + # method="curl") + # stopifnot(file.exists(f.load)) + } + # Load genomic coordinates. + cat("\nUsing database:\n") + cat(paste(f.load, "\n", sep="")) + load(f.load) # load coordinates into variable: genome.coord + + } else if(reg2plot == 'bed') { + rnaseq.gb <- FALSE + } + + # Identify unique regions. + reg.list <- as.factor(ctg.tbl$glist) + uniq.reg <- levels(reg.list) + + # Determine plot coordinates for each unique region. + coord.list <- vector('list', length(uniq.reg)) + names(coord.list) <- uniq.reg + + ReadBedCoord <- function(bed.file) { + # Read a bed into memory as a dataframe. + # Args: + # bed.file: path of the bed file to be read. + # Returns: genome coordinates as a dataframe. + + if(!galaxy && + length(grep("\\.bed([0-9]+)?$", bed.file, ignore.case=T)) == 0) { + warning(sprintf("File name: '%s' does not seem to a correct name +for bed file.\n", bed.file)) + } + bed.coord <- read.table(bed.file, sep="\t", quote="\"") + if(ncol(bed.coord) <3){ + stop("A bed file must contain at least 3 columns! The format is: + chrom, start, end, gname, tid, strand. Columns 4-6 are optional\n") + } + genome.coord <- data.frame(chrom=chromFormat(bed.coord[, 1]), + start=bed.coord[, 2] + 1, + end=bed.coord[, 3], + gid=NA, gname='N', tid='N', strand='+', + byname.uniq=T, bygid.uniq=NA) + # Perform sanity check for bed file. + if(!all(genome.coord$start <= genome.coord$end)) { + stop(sprintf("Sanity check for bed file: %s failed. Bed files are + 0-based and right-side open.\n", bed.file)) + } + + # Deal with columns 4-6 (Optional). + if(ncol(bed.coord) >=4){ + genome.coord$gname <- bed.coord[, 4] + } + if(ncol(bed.coord) >=5){ + genome.coord$tid <- bed.coord[, 5] + } + if(ncol(bed.coord) >=6){ + genome.coord$strand <- bed.coord[, 6] + } + + genome.coord + } + + # Sample a vector but preserve its original sequential order. + sampleInSequence <- function(x, samprate) { + x[ifelse(runif(length(x)) <= samprate, T, F)] + } + + ValidateGeneSubset <- function(gid.match, tid.match, gname.match) { + # To validate that there is no ambiguous hits in gene match. + # Args: + # XXX.match: positional hits with respect to the gene database. 0 means + # no hit. + + subset.matrix <- rbind(gid.match, tid.match, gname.match) + g.valid <- sapply(subset.matrix, function(col.hits) { + length(unique(col.hits[col.hits > 0])) <= 1 + }) + + all(g.valid) + } + + for(i in 1:length(uniq.reg)) { + ur <- uniq.reg[i] + + if(reg2plot == "bed") { + coord.list[[i]] <- ReadBedCoord(ur) + } else if(ur == '-1') { # use whole genome. + coord.list[[i]] <- genome.coord[genome.coord$byname.uniq, ] + } else { # read gene list from text file. + gene.list <- read.table(ur, as.is=T, comment.char='#')$V1 + gid.match <- match(gene.list, genome.coord$gid, nomatch=0) + gname.match <- match(gene.list, genome.coord$gname, nomatch=0) + tid.match <- match(gene.list, genome.coord$tid, nomatch=0) + if(!ValidateGeneSubset(gid.match, tid.match, gname.match)) { + stop("\nAmbiguous hits in gene database. This shall never + happen! Contact ngs.plot maintainers.\n") + } + subset.idx <- pmax(gid.match, tid.match, gname.match) + # subset.idx <- gid.match + tid.match + gname.match + subset.idx <- subset.idx[subset.idx != 0] + if(length(subset.idx) == 0) { + stop("\nGene subset size becomes zero. Are you using the + correct database?\n") + } + coord.list[[i]] <- genome.coord[subset.idx, ] + } + + # Do sampling. + if(samprate < 1) { + samp.idx <- sampleInSequence(1:nrow(coord.list[[i]]), samprate) + coord.list[[i]] <- coord.list[[i]][samp.idx, ] + } + } + + # If bed file, set boolean tag for point interval, i.e. interval=1bp. + if(reg2plot == "bed") { + pint <- all(sapply(coord.list, function(cd) all(cd$start == cd$end))) + if(pint) { + Labs <- c("Center") + } else { + Labs <- c("5'End", "3'End") + } + } + + # Set boolean tag for large interval display. + if(!pint && is.na(lgint)) { + if(median(sapply(coord.list, function(cd) { + median(cd$end - cd$start + 1) + })) > flanksize) { + lgint <- 1 + } else { + lgint <- 0 + } + } + + res <- list(coord.list=coord.list, rnaseq.gb=rnaseq.gb, lgint=lgint, + reg.list=reg.list, uniq.reg=uniq.reg, pint=pint, Labs=Labs) + + # Add exon models to the result if RNA-seq. + if(rnaseq.gb) { + em.load <- file.path(prefix, paste(genome, database, 'exonmodel.RData', + sep='.')) + load(em.load) # load exon models into variable: exonmodel + res$exonmodel <- exonmodel + } + + res +} + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/parse.args.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,521 @@ +# Parse command line arguments and extract them into an associate array. +# Check if the required arguments are all satisfied. +parseArgs <- function(args, manditories) { + if(length(args) %% 2 == 1 || length(args) == 0) { + cat('Unpaired argument and value.\n') + return(NULL) + } + n.i <- seq(1, length(args), by=2) + v.i <- seq(2, length(args), by=2) + args.name <- args[n.i] + args.value <- args[v.i] + + # Check if required argument values are supplied. + miss_tag <- F + man.bool <- manditories %in% args.name + if(!all(man.bool)){ + cat(paste('Missing argument: ', paste(manditories[!man.bool], + collapse=','), '.', sep='') + ) + miss_tag <- T + } + if(miss_tag){ + res <- NULL + }else{ + res <- args.value + names(res) <- args.name + } + res +} + +ConfigTbl <- function(args.tbl, fraglen) { +# Create configuration table from "-C" argument. +# Args: +# args.tbl: named vector of program arguments. +# fraglen: fragment length. +# Returns: dataframe of configuration. + + covfile <- args.tbl['-C'] + + suppressWarnings( + ctg.tbl <- tryCatch( + read.table(covfile, colClasses='character', comment.char='#'), + error=function(e) { + if('-E' %in% names(args.tbl)) { + glist <- args.tbl['-E'] + } else { + glist <- '-1' + } + if('-T' %in% names(args.tbl)) { + title <- args.tbl['-T'] + } else { + title <- 'Noname' + } + data.frame(cov=covfile, glist=glist, title=title, + fraglen=as.character(fraglen), + color=NA, stringsAsFactors=F) + } + ) + ) + + # Read a config file. + if(ncol(ctg.tbl) < 3) { + stop("Configuration file must contain at least 3 columns! +Insufficient information provided.\n") + } + colnames(ctg.tbl)[1:3] <- c('cov', 'glist', 'title') + if(ncol(ctg.tbl) >= 4) { + colnames(ctg.tbl)[4] <- 'fraglen' + fraglen.sp <- strsplit(ctg.tbl$fraglen, ":") + if(!all(sapply(fraglen.sp, function(x) { + length(x) == 1 || length(x) == 2}))) { + stop("Fragment length format must be X or X:Y; X and Y are +integers.\n") + } + if(!all(as.integer(unlist(fraglen.sp)) > 0)) { + stop("Fragment length must be positive integers! Check your +configuration file.\n") + } + } else { + ctg.tbl <- data.frame(ctg.tbl, fraglen=as.character(fraglen), + stringsAsFactors=F) + } + if(ncol(ctg.tbl) >= 5) { + colnames(ctg.tbl)[5] <- 'color' + # Validate color specifications. + col.validated <- col2rgb(ctg.tbl$color) + } else { + ctg.tbl <- data.frame(ctg.tbl, color=NA) + } + ctg.tbl +} + +CheckRegionAllowed <- function(reg2plot, anno.tbl) { +# Check if region to plot is an allowed value. + + region.allowed <- c(as.vector(unique(anno.tbl$Region)), "bed") + if(!reg2plot %in% region.allowed) { + stop(paste(c("Unknown region specified. Must be one of:", + region.allowed, "\n"), collapse=" ")) + } +} + +CoverageVars <- function(args.tbl, reg2plot) { +# Setup variables from program arguments. +# Args: +# args.tbl: named vector of program arguments. +# reg2plot: string describing region to plot. +# Returns: list of variables. + + vl <- list() # vl: configured variable list + + #### Switch for debug #### + if('-Debug' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-Debug']) >= 0) + vl$debug <- as.integer(args.tbl['-Debug']) + } else { + vl$debug <- as.integer(0) + } + + #### Switch for Galaxy usage #### + if('-Galaxy' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-Galaxy']) >= 0) + vl$galaxy <- as.integer(args.tbl['-Galaxy']) + vl$avgname <- args.tbl['-O2'] + vl$heatmapname <- args.tbl['-O3'] + } else { + vl$galaxy <- as.integer(0) + } + + ######## Coverage-generation parameters ######## + #### Flanking region size. #### + if('-L' %in% names(args.tbl)){ + vl$flanksize <- as.integer(args.tbl['-L']) + stopifnot(vl$flanksize >= 0) + } else { + flank.tbl <- setNames( + c(2000, 2000, 2000, 500, 500, 1500, 1000, 1000), + c('tss','tes','genebody','exon','cgi', 'enhancer', 'dhs','bed')) + vl$flanksize <- as.integer(flank.tbl[reg2plot]) + } + + #### Flanking size factor. #### + if('-N' %in% names(args.tbl) && !('-L' %in% names(args.tbl))) { + stopifnot(as.numeric(args.tbl['-N']) >= 0) + vl$flankfactor <- as.numeric(args.tbl['-N']) + } else { + vl$flankfactor <- 0.0 + } + + #### Robust statistics. #### + if('-RB' %in% names(args.tbl)){ + stopifnot(as.numeric(args.tbl['-RB']) >= 0) + vl$robust <- as.numeric(args.tbl['-RB']) + }else{ + vl$robust <- .0 # percentage to be trimmed on both ends. + } + + #### Random sampling rate. #### + if('-S' %in% names(args.tbl)){ + vl$samprate <- as.numeric(args.tbl['-S']) + stopifnot(vl$samprate > 0 && vl$samprate <= 1) + }else{ + vl$samprate <- 1.0 + } + + ##### Set cores number. #### + if('-P' %in% names(args.tbl)){ + stopifnot(as.integer(args.tbl['-P']) >= 0) + vl$cores.number <- as.integer(args.tbl['-P']) + }else{ + vl$cores.number <- as.integer(0) + } + + #### Algorithm for coverage vector normalization #### + if('-AL' %in% names(args.tbl)) { + vl$cov.algo <- args.tbl['-AL'] + al.allowed <- c('spline', 'bin') + stopifnot(vl$cov.algo %in% al.allowed) + } else { + vl$cov.algo <- 'spline' + } + + #### Gene chunk size #### + if('-CS' %in% names(args.tbl)) { + vl$gcs <- as.integer(args.tbl['-CS']) + stopifnot(vl$gcs > 0) + } else { + vl$gcs <- 100 + } + + #### Mapping quality cutoff #### + if('-MQ' %in% names(args.tbl)) { + vl$map.qual <- as.integer(args.tbl['-MQ']) + stopifnot(vl$map.qual >= 0) + } else { + vl$map.qual <- 20 + } + + #### Fragment length #### + if('-FL' %in% names(args.tbl)) { + vl$fraglen <- as.integer(args.tbl['-FL']) + stopifnot(vl$fraglen > 0) + } else { + vl$fraglen <- 150 + } + vl$bufsize <- vl$fraglen # buffer added to both ends of the coverage vec. + + #### Strand-specific coverage #### + if('-SS' %in% names(args.tbl)) { + spec.allowed <- c('both', 'same', 'opposite') + stopifnot(args.tbl['-SS'] %in% spec.allowed) + vl$strand.spec <- args.tbl['-SS'] + } else { + vl$strand.spec <- 'both' + } + + #### Shall interval size be larger than flanking size? #### + if('-IN' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-IN']) >= 0) + vl$inttag <- as.integer(args.tbl['-IN']) + } else { + vl$inttag <- NA + } + + #### Image output forbidden tag. #### + if('-FI' %in% names(args.tbl)){ + stopifnot(as.integer(args.tbl['-FI']) >= 0) + vl$fi_tag <- as.integer(args.tbl['-FI']) + }else{ + vl$fi_tag <- as.integer(0) + } + + vl +} + +PlotVars <- function(args.tbl, existing.vl=vector('character'), + prof.misc=list(), low.count=NULL, go.paras=list()) { +# Setup replot variables. +# Args: +# args.tbl: argument table. +# existing.vl: existing variable name character list. +# prof.misc: misc. avg prof variable list. +# go.paras: gene ordering parameters. +# Returns: list of updated variables. + + ## Plotting-related parameters: + updated.vl <- list() + ### Misc. parameters: + #### Font size. #### + if('-FS' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-FS']) > 0) + updated.vl$font.size <- as.integer(args.tbl['-FS']) + } else if(!'font.size' %in% existing.vl) { + updated.vl$font.size <- 12 + } + + ### Avg. profiles parameters: + #### Plot width. #### + if('-WD' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-WD']) > 0) + updated.vl$plot.width <- as.integer(args.tbl['-WD']) + } else if(!'plot.width' %in% existing.vl) { + updated.vl$plot.width <- 8 + } + + #### Plot height. #### + if('-HG' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-HG']) > 0) + updated.vl$plot.height <- as.integer(args.tbl['-HG']) + } else if(!'plot.height' %in% existing.vl) { + updated.vl$plot.height <- 7 + } + + #### Shall standard errors be plotted around average profiles? #### + if('-SE' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-SE']) >= 0) + updated.vl$se <- as.integer(args.tbl['-SE']) + } else if(!'se' %in% existing.vl) { + updated.vl$se <- 1 + } + + #### Smooth function radius. #### + if('-MW' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-MW']) >= 1) + updated.vl$mw <- as.integer(args.tbl['-MW']) + } else if(!'mw' %in% existing.vl) { + updated.vl$mw <- 1 + } + + #### Shaded area alpha. #### + if('-H' %in% names(args.tbl)) { + stopifnot(as.numeric(args.tbl['-H']) >= 0 && + as.numeric(args.tbl['-H']) < 1) + updated.vl$shade.alp <- as.numeric(args.tbl['-H']) + } else if(!'shade.alp' %in% existing.vl) { + updated.vl$shade.alp <- 0 + } + + #### Misc. options for avg. profiles. #### + updated.vl$prof.misc <- prof.misc + if('-YAS' %in% names(args.tbl)) { + ystr <- args.tbl['-YAS'] + if(ystr != 'auto') { + yp <- unlist(strsplit(ystr, ',')) + if(length(yp) == 2) { + y.min <- as.numeric(yp[1]) + y.max <- as.numeric(yp[2]) + stopifnot(y.min < y.max) + } else { + stop("-YAS must be 'auto' or a pair of numerics separated +by ','\n") + } + updated.vl$prof.misc$yscale <- c(y.min, y.max) + } else { + updated.vl$prof.misc$yscale <- 'auto' + } + } else if(!'yscale' %in% names(prof.misc)) { + updated.vl$prof.misc$yscale <- 'auto' + } + if('-LEG' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-LEG']) >= 0) + updated.vl$prof.misc$legend <- as.integer(args.tbl['-LEG']) + } else if(!'legend' %in% names(prof.misc)) { + updated.vl$prof.misc$legend <- T + } + if('-BOX' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-BOX']) >= 0) + updated.vl$prof.misc$box <- as.integer(args.tbl['-BOX']) + } else if(!'box' %in% names(prof.misc)) { + updated.vl$prof.misc$box <- T + } + if('-VLN' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-VLN']) >= 0) + updated.vl$prof.misc$vline <- as.integer(args.tbl['-VLN']) + } else if(!'vline' %in% names(prof.misc)) { + updated.vl$prof.misc$vline <- T + } + if('-XYL' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-XYL']) >= 0) + updated.vl$prof.misc$xylab <- as.integer(args.tbl['-XYL']) + } else if(!'xylab' %in% names(prof.misc)) { + updated.vl$prof.misc$xylab <- T + } + if('-LWD' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-LWD']) > 0) + updated.vl$prof.misc$line.wd <- as.integer(args.tbl['-LWD']) + } else if(!'line.wd' %in% names(prof.misc)) { + updated.vl$prof.misc$line.wd <- 3 + } + + ### Heatmap parameters: + #### Gene order algorithm #### + if('-GO' %in% names(args.tbl)){ + go.allowed <- c('total', 'max', 'prod', 'diff', 'hc', 'none', 'km') + stopifnot(args.tbl['-GO'] %in% go.allowed) + updated.vl$go.algo <- args.tbl['-GO'] + } else if(!'go.algo' %in% existing.vl){ + updated.vl$go.algo <- 'total' # hierarchical clustering. + } + + #### Reduce ratio to control a heatmap height #### + if('-RR' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-RR']) > 0) + updated.vl$rr <- as.integer(args.tbl['-RR']) + } else if(!'rr' %in% existing.vl) { + updated.vl$rr <- 30 + } + + #### Color scale string. #### + if('-SC' %in% names(args.tbl)) { + if(!args.tbl['-SC'] %in% c('local', 'region', 'global')) { + scale.pair <- unlist(strsplit(args.tbl['-SC'], ",")) + if(length(scale.pair) != 2 || is.na(as.numeric(scale.pair[1])) || + is.na(as.numeric(scale.pair[2]))) { + stop("Color scale format error: must be local, region, global +or a pair of numerics separated by ','\n") + } + } + updated.vl$color.scale <- args.tbl['-SC'] + } else if(!'color.scale' %in% existing.vl) { + updated.vl$color.scale <- 'local' + } + + #### Flooding fraction. #### + if('-FC' %in% names(args.tbl)) { + stopifnot(as.numeric(args.tbl['-FC']) >= 0 && + as.numeric(args.tbl['-FC']) < 1) + updated.vl$flood.frac <- as.numeric(args.tbl['-FC']) + } else if(!'flood.frac' %in% existing.vl) { + updated.vl$flood.frac <- .02 + } + + #### Heatmap color. #### + if('-CO' %in% names(args.tbl)) { + updated.vl$hm.color <- as.character(args.tbl['-CO']) + } else if(!'hm.color' %in% existing.vl){ + updated.vl$hm.color <- "default" + } + + #### Color distribution. #### + if('-CD' %in% names(args.tbl)) { + stopifnot(as.numeric(args.tbl['-CD']) > 0) + updated.vl$color.distr <- as.numeric(args.tbl['-CD']) + } else if(!'color.distr' %in% existing.vl) { + updated.vl$color.distr <- .6 + } + + #### Low count cutoff for rank-based normalization #### + if('-LOW' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-LOW']) >= 0) + updated.vl$low.count <- as.integer(args.tbl['-LOW']) + } else if(!'low.count' %in% existing.vl) { + updated.vl$low.count <- 10 + } else { # ensure low.count is not empty. + updated.vl$low.count <- low.count + } + if(!is.null(low.count)) { + updated.vl$low.count.ratio <- updated.vl$low.count / low.count + } + + #### Misc. options for heatmap. #### + updated.vl$go.paras <- go.paras + if('-KNC' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-KNC']) > 0) + updated.vl$go.paras$knc <- as.integer(args.tbl['-KNC']) + } else if(!'knc' %in% names(go.paras)) { + updated.vl$go.paras$knc <- 5 + } + if('-MIT' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-MIT']) > 0) + updated.vl$go.paras$max.iter <- as.integer(args.tbl['-MIT']) + } else if(!'max.iter' %in% names(go.paras)) { + updated.vl$go.paras$max.iter <- 20 + } + if('-NRS' %in% names(args.tbl)) { + stopifnot(as.integer(args.tbl['-NRS']) > 0) + updated.vl$go.paras$nrs <- as.integer(args.tbl['-NRS']) + } else if(!'nrs' %in% names(go.paras)) { + updated.vl$go.paras$nrs <- 30 + } + + + updated.vl +} + +CheckHMColorConfig <- function(hm.color, bam.pair) { + if(hm.color != 'default') { + v.colors <- unlist(strsplit(hm.color, ":")) + if(bam.pair && length(v.colors) != 2 && length(v.colors) != 3 || + !bam.pair && length(v.colors) != 1) { + stop("Heatmap color specifications must correspond to bam-pair!\n") + } + } +} + +EchoPlotArgs <- function() { + cat("## Plotting-related parameters:\n") + cat("### Misc. parameters:\n") + cat(" -FS Font size(default=12)\n") + cat("### Avg. profiles parameters:\n") + cat(" -WD Image width(default=8)\n") + cat(" -HG Image height(default=7)\n") + cat(" -SE Shall standard errors be plotted?(0 or 1)\n") + cat(" -MW Moving window width to smooth avg. profiles, must be integer\n") + cat(" 1=no(default); 3=slightly; 5=somewhat; 9=quite; 13=super.\n") + cat(" -H Opacity of shaded area, suggested value:[0, 0.5]\n") + cat(" default=0, i.e. no shading, just lines\n") + cat(" -YAS Y-axis scale: auto(default) or min_val,max_val(custom scale)\n") + cat(" -LEG Draw legend? 1(default) or 0\n") + cat(" -BOX Draw box around plot? 1(default) or 0\n") + cat(" -VLN Draw vertical lines? 1(default) or 0\n") + cat(" -XYL Draw X- and Y-axis labels? 1(default) or 0\n") + cat(" -LWD Line width(default=3)\n") + cat("### Heatmap parameters:\n") + cat(" -GO Gene order algorithm used in heatmaps: total(default), hc, max,\n") + cat(" prod, diff, km and none(according to gene list supplied)\n") + cat(" -LOW Low count cutoff(default=10) in rank-based normalization\n") + cat(" -KNC K-means or HC number of clusters(default=5)\n") + cat(" -MIT Maximum number of iterations(default=20) for K-means\n") + cat(" -NRS Number of random starts(default=30) in K-means\n") + cat(" -RR Reduce ratio(default=30). The parameter controls the heatmap height\n") + cat(" The smaller the value, the taller the heatmap\n") + cat(" -SC Color scale used to map values to colors in a heatmap\n") + cat(" local(default): base on each individual heatmap\n") + cat(" region: base on all heatmaps belong to the same region\n") + cat(" global: base on all heatmaps together\n") + cat(" min_val,max_val: custom scale using a pair of numerics\n") + cat(" -FC Flooding fraction:[0, 1), default=0.02\n") + cat(" -CO Color for heatmap. For bam-pair, use color-tri(neg_color:[neu_color]:pos_color)\n") + cat(" Hint: must use R colors, such as darkgreen, yellow and blue2\n") + cat(" The neutral color is optional(default=black)\n") + cat(" -CD Color distribution for heatmap(default=0.6). Must be a positive number\n") + cat(" Hint: lower values give more widely spaced colors at the negative end\n") + cat(" In other words, they shift the neutral color to positive values\n") + cat(" If set to 1, the neutral color represents 0(i.e. no bias)\n") + +} + +EchoCoverageArgs <- function() { + cat("## Coverage-generation parameters:\n") + cat(" -F Further information provided to select database table or plottype:\n") + cat(" This is a string of description separated by comma.\n") + cat(" E.g. protein_coding,K562,rnaseq(order of descriptors does not matter)\n") + cat(" means coding genes in K562 cell line drawn in rnaseq mode.\n") + cat(" -D Gene database: ensembl(default), refseq\n") + cat(" -L Flanking region size(will override flanking factor)\n") + cat(" -N Flanking region factor\n") + cat(" -RB The fraction of extreme values to be trimmed on both ends\n") + cat(" default=0, 0.05 means 5% of extreme values will be trimmed\n") + cat(" -S Randomly sample the regions for plot, must be:(0, 1]\n") + cat(" -P #CPUs to use. Set 0(default) for auto detection\n") + cat(" -AL Algorithm used to normalize coverage vectors: spline(default), bin\n") + cat(" -CS Chunk size for loading genes in batch(default=100)\n") + cat(" -MQ Mapping quality cutoff to filter reads(default=20)\n") + cat(" -FL Fragment length used to calculate physical coverage(default=150)\n") + cat(" -SS Strand-specific coverage calculation: both(default), same, opposite\n") + cat(" -IN Shall interval be larger than flanking in plot?(0 or 1, default=automatic)\n") + cat(" -FI Forbid image output if set to 1(default=0)\n") +} +############### End arguments configuration ##################### +#################################################################
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/plotlib.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,649 @@ +#### plotlib.r #### +# This contains the library for plotting related functions. +# +# Authors: Li Shen, Ningyi Shao +# +# Created: Feb 19, 2013 +# Last updated: May 21, 2013 +# + +SetupHeatmapDevice <- function(reg.list, uniq.reg, ng.list, pts, font.size=12, + unit.width=4, reduce.ratio=30) { +# Configure parameters for heatmap output device. The output is used by +# external procedures to setup pdf device ready for heatmap plotting. +# Args: +# reg.list: region list as in config file. +# uniq.reg: unique region list. +# ng.list: number of genes per heatmap in the order as config file. +# pts: data points (number of columns of heatmaps). +# font.size: font size. +# unit.width: image width per heatmap. +# reduce.ratio: how compressed are genes in comparison to data points? This +# controls image height. + + # Number of plots per region. + reg.np <- sapply(uniq.reg, function(r) sum(reg.list==r)) + + # Number of genes per region. + reg.ng <- sapply(uniq.reg, function(r) { + ri <- which(reg.list==r)[1] + ng.list[ri] + }) + + # Adjustment ratio. + origin.fs <- 12 # default font size. + fs.adj.ratio <- font.size / origin.fs + # Margin size (in lines) adjusted by ratio. + m.bot <- fs.adj.ratio * 2 + m.lef <- fs.adj.ratio * 1.5 + m.top <- fs.adj.ratio * 2 + m.rig <- fs.adj.ratio * 1.5 + key.in <- fs.adj.ratio * 1.0 # colorkey in inches. + m.lef.diff <- (fs.adj.ratio - 1) * 1.5 + m.rig.diff <- (fs.adj.ratio - 1) * 1.5 + # Setup image size. + hm.width <- (unit.width + m.lef.diff + m.rig.diff) * max(reg.np) + ipl <- .2 # inches per line. Obtained from par->'mai', 'mar'. + # Convert #gene to image height. + reg.hei <- sapply(reg.ng, function(r) { + c(key.in, # colorkey + margin. + r * unit.width / pts / reduce.ratio + + m.bot * ipl + m.top * ipl) # heatmap + margin. + }) + reg.hei <- c(reg.hei) + hm.height <- sum(reg.hei) + + # Setup layout of the heatmaps. + lay.mat <- matrix(0, ncol=max(reg.np), nrow=length(reg.np) * 2) + fig.n <- 1 # figure plotting number. + for(i in 1:length(reg.np)) { + row.upper <- i * 2 - 1 + row.lower <- i * 2 + for(j in 1:reg.np[i]) { + lay.mat[row.upper, j] <- fig.n; + fig.n <- fig.n + 1 + lay.mat[row.lower, j] <- fig.n; + fig.n <- fig.n + 1 + } + } + + list(reg.hei=reg.hei, hm.width=hm.width, hm.height=hm.height, + lay.mat=lay.mat, heatmap.mar=c(m.bot, m.lef, m.top, m.rig) * ipl) +} + +SetPtsSpline <- function(pint, lgint) { +# Set data points for spline function. +# Args: +# pint: tag for point interval. +# Return: list of data points, middle data points, flanking data points. + + pts <- 100 # data points to plot: 0...pts + if(pint){ # point interval. + m.pts <- 1 # middle part points. + f.pts <- pts / 2 # flanking part points. + } else { + if(lgint) { + m.pts <- pts / 5 * 3 + 1 + f.pts <- pts / 5 + 1 + } else { + m.pts <- pts / 5 + 1 + f.pts <- pts / 5 * 2 + 1 + } + } + list(pts=pts, m.pts=m.pts, f.pts=f.pts) +} + +CreatePlotMat <- function(pts, ctg.tbl) { +# Create matrix for avg. profiles. +# Args: +# pts: data points. +# ctg.tbl: configuration table. +# Return: avg. profile matrix initialized to zero. + + regcovMat <- matrix(0, nrow=pts + 1, ncol=nrow(ctg.tbl)) + colnames(regcovMat) <- ctg.tbl$title + regcovMat +} + +CreateConfiMat <- function(se, pts, ctg.tbl){ +# Create matrix for standard errors. +# Args: +# se: tag for standard error plotting. +# pts: data points. +# ctg.tbl: configuration table. +# Return: standard error matrix initialized to zero or null. + + if(se){ + confiMat <- matrix(0, nrow=pts + 1, ncol=nrow(ctg.tbl)) + colnames(confiMat) <- ctg.tbl$title + } else { + confiMat <- NULL + } + confiMat +} + +col2alpha <- function(col2use, alpha){ +# Convert a vector of solid colors to semi-transparent colors. +# Args: +# col2use: vector of colors. +# alpha: represents degree of opacity - [0,1] +# Return: vector of transformed colors. + + apply(col2rgb(col2use), 2, function(x){ + rgb(x[1], x[2], x[3], alpha=alpha*255, maxColorValue=255) + }) +} + +smoothvec <- function(v, radius, method=c('mean', 'median')){ +# Given a vector of coverage, return smoothed version of coverage. +# Args: +# v: vector of coverage +# radius: fraction of org. vector size. +# method: smooth method +# Return: vector of smoothed coverage. + + stopifnot(is.vector(v)) + stopifnot(length(v) > 0) + stopifnot(radius > 0 && radius < 1) + + halfwin <- ceiling(length(v) * radius) + s <- rep(NA, length(v)) + + for(i in 1:length(v)){ + winpos <- (i - halfwin) : (i + halfwin) + winpos <- winpos[winpos > 0 & winpos <= length(v)] + if(method == 'mean'){ + s[i] <- mean(v[winpos]) + }else if(method == 'median'){ + s[i] <- median(v[winpos]) + } + } + s +} + +smoothplot <- function(m, radius, method=c('mean', 'median')){ +# Smooth the entire avg. profile matrix using smoothvec. +# Args: +# m: avg. profile matrix +# radius: fraction of org. vector size. +# method: smooth method. +# Return: smoothed matrix. + + stopifnot(is.matrix(m) || is.vector(m)) + + if(is.matrix(m)) { + for(i in 1:ncol(m)) { + m[, i] <- smoothvec(m[, i], radius, method) + } + } else { + m <- smoothvec(m, radius, method) + } + m +} + +genXticks <- function(reg2plot, pint, lgint, pts, flanksize, flankfactor, + Labs) { +# Generate X-ticks for plotting. +# Args: +# reg2plot: string representation of region. +# pint: point interval. +# lgint: tag for large interval. +# pts: data points. +# flanksize: flanking region size in bps. +# flankfactor: flanking region factor. +# Labs: character vector of labels of the genomic region. +# Return: list of x-tick position and label. + + if(pint){ # point interval. + mid.lab <- Labs[1] + tick.pos <- c(0, pts / 4, pts / 2, pts / 4 * 3, pts) + tick.lab <- as.character(c(-flanksize, -flanksize/2, mid.lab, + flanksize/2, flanksize)) + }else{ + left.lab <- Labs[1] + right.lab <- Labs[2] + tick.pos <- c(0, pts / 5, pts / 5 * 2, pts / 5 * 3, pts / 5 * 4, pts) + if(lgint){ # large interval: fla int int int fla + if(flankfactor > 0){ # show percentage at x-tick. + tick.lab <- c(sprintf("%d%%", -flankfactor*100), + left.lab, '33%', '66%', right.lab, + sprintf("%d%%", flankfactor*100)) + } else{ # show bps at x-tick. + tick.lab <- c(as.character(-flanksize), + left.lab, '33%', '66%', right.lab, + as.character(flanksize)) + } + } else { # small interval: fla fla int fla fla. + if(flankfactor > 0){ + tick.lab <- c(sprintf("%d%%", -flankfactor*100), + sprintf("%d%%", -flankfactor*50), + left.lab, right.lab, + sprintf("%d%%", flankfactor*50), + sprintf("%d%%", flankfactor*100)) + } else { + tick.lab <- c(as.character(-flanksize), + as.character(-flanksize/2), + left.lab, right.lab, + as.character(flanksize/2), + as.character(flanksize)) + } + } + } + list(pos=tick.pos, lab=tick.lab) +} + +plotmat <- function(regcovMat, title2plot, plot.colors, bam.pair, xticks, + pts, m.pts, f.pts, pint, shade.alp=0, confiMat=NULL, mw=1, + misc.options=list(yscale='auto', legend=T, box=T, vline=T, + xylab=T, line.wd=3)) { +# Plot avg. profiles and standard errors around them. +# Args: +# regcovMat: matrix for avg. profiles. +# title2plot: profile names, will be shown in figure legend. +# plot.colors: vector of color specifications for all curves. +# bam.pair: boolean for bam-pair data. +# xticks: X-axis ticks. +# pts: data points +# m.pts: middle part data points +# f.pts: flanking part data points +# pint: tag for point interval +# shade.alp: shading area alpha +# confiMat: matrix for standard errors. +# mw: moving window size for smoothing function. +# misc.options: list of misc. options - y-axis scale, legend, box around plot, +# verticle lines, X- and Y-axis labels, line width. + + # Smooth avg. profiles if specified. + if(mw > 1){ + regcovMat <- as.matrix(runmean(regcovMat, k=mw, alg='C', + endrule='mean')) + } + + # Choose colors. + if(any(is.na(plot.colors))) { + ncurve <- ncol(regcovMat) + if(ncurve <= 8) { + suppressMessages(require(RColorBrewer, warn.conflicts=F)) + col2use <- brewer.pal(ifelse(ncurve >= 3, ncurve, 3), 'Dark2') + col2use <- col2use[1:ncurve] + } else { + col2use <- rainbow(ncurve) + } + } else { + col2use <- plot.colors + } + col2use <- col2alpha(col2use, 0.8) + + # Plot profiles. + ytext <- ifelse(bam.pair, "log2(Fold change vs. control)", + "Read count Per Million mapped reads") + xrange <- 0:pts + y.lim <- NULL + if(length(misc.options$yscale) == 2) { + y.lim <- misc.options$yscale + } + matplot(xrange, regcovMat, + xaxt='n', type="l", col=col2use, ylim=y.lim, + lty="solid", lwd=misc.options$line.wd, frame.plot=F, ann=F) + if(misc.options$xylab) { + title(xlab="Genomic Region (5' -> 3')", ylab=ytext) + } + axis(1, at=xticks$pos, labels=xticks$lab, lwd=3, lwd.ticks=3) + if(misc.options$box) { + # box around plot. + box() + } + + # Add shade area. + if(shade.alp > 0){ + for(i in 1:ncol(regcovMat)){ + v.x <- c(xrange[1], xrange, xrange[length(xrange)]) + v.y <- regcovMat[, i] + v.y <- c(0, v.y, 0) + col.rgb <- col2rgb(col2use[i]) + p.col <- rgb(col.rgb[1, 1], col.rgb[2, 1], col.rgb[3, 1], + alpha=shade.alp * 255, maxColorValue=255) + polygon(v.x, v.y, density=-1, border=NA, col=p.col) + } + } + + # Add standard errors. + if(!is.null(confiMat)){ + v.x <- c(xrange, rev(xrange)) + for(i in 1:ncol(confiMat)){ + v.y <- c(regcovMat[, i] + confiMat[, i], + rev(regcovMat[, i] - confiMat[, i])) + col.rgb <- col2rgb(col2use[i]) + p.col <- rgb(col.rgb[1, 1], col.rgb[2, 1], col.rgb[3, 1], + alpha=0.2 * 255, maxColorValue=255) + polygon(v.x, v.y, density=-1, border=NA, col=p.col) + } + } + + if(misc.options$vline) { + # Add gray lines indicating feature boundaries. + if(pint) { + abline(v=f.pts, col="gray", lwd=2) + } else { + abline(v=f.pts - 1, col="gray", lwd=2) + abline(v=f.pts + m.pts - 2, col="gray", lwd=2) + } + } + + if(misc.options$legend) { + # Legend. + legend("topright", title2plot, text.col=col2use) + } +} + +spline_mat <- function(mat, n=100){ +# Calculate splined coverage for a matrix. +# Args: +# mat: each column represents a profile to be interpolated. +# n: number of data points to be interpolated. + + foreach(r=iter(mat, by='row'), + .combine='rbind', .multicombine=T) %dopar% { + spline(1:length(r), r, n)$y + } +} + +RankNormalizeMatrix <- function(mat, low.cutoff) { +# Rank-based normalization for a data matrix. +# Args: +# mat: data matrix. +# low.cutoff: low value cutoff. +# Return: rank normalized matrix. + + stopifnot(is.matrix(mat)) + + concat.dat <- c(mat) + low.mask <- concat.dat < low.cutoff + concat.r <- rank(concat.dat) + concat.r[low.mask] <- 0 + + matrix(concat.r, nrow=nrow(mat)) +} + +OrderGenesHeatmap <- function(enrichList, lowCutoffs, + method=c('total', 'max', 'prod', 'diff', 'hc', + 'none', 'km'), + go.paras=list(knc=5, max.iter=20, nrs=30)) { +# Order genes with a list of heatmap data. +# Args: +# enrichList: heatmap data in a list. +# lowCutoffs: low count cutoff for normalized count data. +# method: algorithm used to order genes. +# go.paras: gene ordering parameters. +# Returns: a vector of REVERSED gene orders. +# NOTE: due to the design of image function, the order needs to be reversed +# so that the genes will be shown correctly. + + rankList <- mapply(RankNormalizeMatrix, + mat=enrichList, low.cutoff=lowCutoffs, SIMPLIFY=F) + np <- length(enrichList) + + if(method == 'hc') { + rankCombined <- do.call('cbind', rankList) + # Clustering and order genes. + hc <- hclust(dist(rankCombined, method='euclidean'), + method='complete') + memb <- cutree(hc, k = go.paras$knc) + list(rev(hc$order), memb) # reversed! + } else if(method == 'km') { + rankCombined <- do.call('cbind', rankList) + km <- kmeans(rankCombined, centers=go.paras$knc, + iter.max=go.paras$max.iter, nstart=go.paras$nrs) + list(rev(order(km$cluster)), km$cluster) # reversed! + } else if(method == 'total' || method == 'diff' && np == 1) { + list(order(rowSums(rankList[[1]])), NULL) + } else if(method == 'max') { # peak enrichment value of the 1st profile. + list(order(apply(rankList[[1]], 1, max)), NULL) + } else if(method == 'prod') { # product of all profiles. + rs.mat <- sapply(rankList, rowSums) + g.prod <- apply(rs.mat, 1, prod) + list(order(g.prod), NULL) + } else if(method == 'diff' && np > 1) { # difference between 2 profiles. + list(order(rowSums(rankList[[1]]) - rowSums(rankList[[2]])), NULL) + } else if(method == 'none') { # according to the order of input gene list. + # Because the image function draws from bottom to top, the rows are + # reversed to give a more natural look. + list(rev(1:nrow(enrichList[[1]])),NULL) + } else { + # pass. + } +} + + +plotheat <- function(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, + go.paras, title2plot, bam.pair, xticks, flood.q=.02, + do.plot=T, hm.color="default", color.distr=.6, + color.scale='local') { +# Plot heatmaps with genes ordered according to some algorithm. +# Args: +# reg.list: factor vector of regions as in configuration. +# uniq.reg: character vector of unique regions. +# enrichList: list of heatmap data. +# v.low.cutoff: low count cutoff for normalized count data. +# go.algo: gene order algorithm. +# go.paras: gene ordering parameters. +# title2plot: title for each heatmap. Same as the legends in avgprof. +# bam.pair: boolean tag for bam-pair. +# xticks: info for X-axis ticks. +# flood.q: flooding percentage. +# do.plot: boolean tag for plotting heatmaps. +# hm.color: string for heatmap colors. +# color.distr: positive number for color distribution. +# color.scale: string for the method to adjust color scale. +# Returns: ordered gene names for each unique region as a list. + + # Setup basic parameters. + ncolor <- 256 + if(bam.pair) { + if(hm.color != "default") { + tri.colors <- unlist(strsplit(hm.color, ':')) + neg.color <- tri.colors[1] + if(length(tri.colors) == 2) { + neu.color <- 'black' + pos.color <- tri.colors[2] + } else { + neu.color <- tri.colors[2] + pos.color <- tri.colors[3] + } + enrich.palette <- colorRampPalette(c(neg.color, neu.color, + pos.color), + bias=color.distr, + interpolate='spline') + } else { + enrich.palette <- colorRampPalette(c('blue', 'black', 'yellow'), + bias=color.distr, + interpolate='spline') + } + } else { + if(hm.color != "default") { + enrich.palette <- colorRampPalette(c('snow', hm.color)) + } else { + enrich.palette <- colorRampPalette(c('snow', 'red2')) + } + } + + hm_cols <- ncol(enrichList[[1]]) + + # Adjust X-axis tick position. In a heatmap, X-axis is [0, 1]. + # Assume xticks$pos is from 0 to N(>0). + xticks$pos <- xticks$pos / tail(xticks$pos, n=1) # scale to the same size. + + # Define a function to calculate color breaks. + ColorBreaks <- function(max.e, min.e, bam.pair, ncolor) { + # Args: + # max.e: maximum enrichment value to be mapped to color. + # min.e: minimum enrichment value to be mapped to color. + # bam.pair: boolean tag for bam-pair. + # ncolor: number of colors to use. + # Returns: vector of color breaks. + + # If bam-pair is used, create breaks for positives and negatives + # separately. If log2 ratios are all positive or negative, use only + # half of the color space. + if(bam.pair) { + max.e <- ifelse(max.e > 0, max.e, 1) + min.e <- ifelse(min.e < 0, min.e, -1) + c(seq(min.e, 0, length.out=ncolor / 2 + 1), + seq(0, max.e, length.out=ncolor / 2 + 1)[-1]) + } else { + seq(min.e, max.e, length.out=ncolor + 1) + } + } + + if(grepl(",", color.scale)) { + scale.pair <- unlist(strsplit(color.scale, ",")) + scale.min <- as.numeric(scale.pair[1]) + scale.max <- as.numeric(scale.pair[2]) + if(scale.min >= scale.max) { + warning("Color scale min value is >= max value.\n") + } + flood.pts <- c(scale.min, scale.max) + brk.use <- ColorBreaks(scale.max, scale.min, bam.pair, ncolor) + } + + # If color scale is global, calculate breaks and quantile here. + if(color.scale == 'global') { + flood.pts <- quantile(c(enrichList, recursive=T), c(flood.q, 1-flood.q)) + brk.use <- ColorBreaks(flood.pts[2], flood.pts[1], bam.pair, ncolor) + } + + # Go through each unique region. + # Do NOT use "dopar" in the "foreach" loops here because this will disturb + # the image order. + go.list <- vector('list', length(uniq.reg)) + go.cluster <- vector('list', length(uniq.reg)) + + names(go.list) <- uniq.reg + names(go.cluster) <- uniq.reg + + for(ur in uniq.reg) { + # ur <- uniq.reg[i] + plist <- which(reg.list==ur) # get indices in the config file. + + # Combine all profiles into one. + # enrichCombined <- do.call('cbind', enrichList[plist]) + enrichSelected <- enrichList[plist] + + # If color scale is region, calculate breaks and quantile here. + if(color.scale == 'region') { + flood.pts <- quantile(c(enrichSelected, recursive=T), + c(flood.q, 1-flood.q)) + brk.use <- ColorBreaks(flood.pts[2], flood.pts[1], bam.pair, ncolor) + } + + # Order genes. + if(is.matrix(enrichSelected[[1]]) && nrow(enrichSelected[[1]]) > 1) { + if(bam.pair) { + lowCutoffs <- 0 + } else { + lowCutoffs <- v.low.cutoff[plist] + } + g.order.list <- OrderGenesHeatmap(enrichSelected, lowCutoffs, + go.algo, go.paras) + g.order <- g.order.list[[1]] + g.cluster <- g.order.list[[2]] + if(is.null(g.cluster)) { + go.cluster[[ur]] <- NA + } else{ + go.cluster[[ur]] <- rev(g.cluster[g.order]) + } + go.list[[ur]] <- rev(rownames(enrichSelected[[1]][g.order, ])) + } else { + go.cluster[[ur]] <- NULL + go.list[[ur]] <- NULL + } + + if(!do.plot) { + next + } + + # Go through each sample and do plot. + for(pj in plist) { + if(!is.null(g.order)) { + enrichList[[pj]] <- enrichList[[pj]][g.order, ] + } + + # If color scale is local, calculate breaks and quantiles here. + if(color.scale == 'local') { + flood.pts <- quantile(c(enrichList[[pj]], recursive=T), + c(flood.q, 1-flood.q)) + brk.use <- ColorBreaks(flood.pts[2], flood.pts[1], bam.pair, + ncolor) + } + + # Flooding extreme values. + enrichList[[pj]][ enrichList[[pj]] < flood.pts[1] ] <- flood.pts[1] + enrichList[[pj]][ enrichList[[pj]] > flood.pts[2] ] <- flood.pts[2] + + # Draw colorkey. + image(z=matrix(brk.use, ncol=1), col=enrich.palette(ncolor), + breaks=brk.use, axes=F, useRaster=T, main='Colorkey') + axis(1, at=seq(0, 1, length.out=5), + labels=format(brk.use[seq(1, ncolor + 1, length.out=5)], + digits=1), + lwd=1, lwd.ticks=1) + + # Draw heatmap. + image(z=t(enrichList[[pj]]), col=enrich.palette(ncolor), + breaks=brk.use, axes=F, useRaster=T, main=title2plot[pj]) + + axis(1, at=xticks$pos, labels=xticks$lab, lwd=1, lwd.ticks=1) + } + } + list(go.list,go.cluster) +} + +trim <- function(x, p){ +# Trim a numeric vector on both ends. +# Args: +# x: numeric vector. +# p: percentage of data to trim. +# Return: trimmed vector. + + low <- quantile(x, p) + hig <- quantile(x, 1 - p) + x[x > low & x < hig] +} + +CalcSem <- function(x, rb=.05){ +# Calculate standard error of mean for a numeric vector. +# Args: +# x: numeric vector +# rb: fraction of data to trim before calculating sem. +# Return: a scalar of the standard error of mean + + if(rb > 0){ + x <- trim(x, rb) + } + sem <- sd(x) / sqrt(length(x)) + ifelse(is.na(sem), 0, sem) + # NOTE: this should be improved to handle exception that "sd" calculation + # emits errors. +} + + + + +## Leave for future reference. +# +# Set the antialiasing. +# type <- NULL +# if (capabilities()["aqua"]) { +# type <- "quartz" +# } else if (capabilities()["cairo"]) { +# type <- "cairo" +# } else if (capabilities()["X11"]) { +# type <- "Xlib" +# } +# Set the output type based on capabilities. +# if (is.null(type)){ +# png(plot.name, width, height, pointsize=pointsize) + +# } else { +# png(plot.name, width, height, pointsize=pointsize, type=type) +# }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngs.plot.r Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,341 @@ +#!/usr/bin/env Rscript +# +# Program: ngs.plot.r +# Purpose: Plot sequencing coverages at different genomic regions. +# Allow overlaying various coverages with gene lists. +# +# -- by Li Shen, MSSM +# Created: Nov 2011. +# -- by Christophe Antoniewski +# recoded for Galaxy: Dec 2017 + +ngsplot.version <- '2.63_artbio' +# Program environment variable. +progpath <- Sys.getenv('NGSPLOT') +if(progpath == "") { + stop("Set environment variable NGSPLOT before run the program. See README + for details.\n") +} + +source(file.path(progpath, 'lib', 'parse.args.r')) +source(file.path(progpath, 'lib', 'genedb.r')) +source(file.path(progpath, 'lib', 'plotlib.r')) +source(file.path(progpath, 'lib', 'coverage.r')) + +# Deal with command line arguments. +cmd.help <- function(){ + cat("\nVisit https://github.com/shenlab-sinai/ngsplot/wiki/ProgramArguments101 for details\n") + cat(paste("Version:", ngsplot.version, sep=" ")) + cat("\nUsage: ngs.plot.r -G genome -R region -C [cov|config]file\n") + cat(" -O name [Options]\n") + cat("\n## Mandatory parameters:\n") + cat(" -G Genome name. Use ngsplotdb.py list to show available genomes.\n") + cat(" -R Genomic regions to plot: tss, tes, genebody, exon, cgi, enhancer, dhs or bed\n") + cat(" -C Indexed bam file or a configuration file for multiplot\n") + cat(" -O Name for output: multiple files will be generated\n") + cat("## Optional parameters related to configuration file:\n") + cat(" -E Gene list to subset regions OR bed file for custom region\n") + cat(" -T Image title\n") + EchoCoverageArgs() + EchoPlotArgs() + cat("\n") +} + + +########################################################################### +#################### Deal with program input arguments #################### +args <- commandArgs(T) +# args <- unlist(strsplit('-G mm10 -R tss -C K27M_no_stim_3_GATCAG_L006_R1_001Aligned.out.srt.rmdup.bam -O test -Debug 1', ' ')) + +# Input argument parser. +args.tbl <- parseArgs(args, c('-G', '-C', '-R', '-O')) # see lib/parse.args.r +if(is.null(args.tbl)){ + cmd.help() + stop('Error in parsing command line arguments. Stop.\n') +} +genome <- args.tbl['-G'] +reg2plot <- args.tbl['-R'] +oname <- args.tbl['-O'] +warning(sprintf("%s", args.tbl)) + +cat("Configuring variables...") +# Load tables of database: default.tbl, dbfile.tbl +default.tbl <- read.delim(file.path(progpath, 'database', 'default.tbl')) +dbfile.tbl <- read.delim(file.path(progpath, 'database', 'dbfile.tbl')) +CheckRegionAllowed(reg2plot, default.tbl) + +# Setup variables from arguments. +cov.args <- CoverageVars(args.tbl, reg2plot) +attach(cov.args) # +plot.args <- PlotVars(args.tbl) +attach(plot.args) + +# Configuration: coverage-genelist-title relationships. +ctg.tbl <- ConfigTbl(args.tbl, fraglen) + +# Setup plot-related coordinates and variables. +plotvar.list <- SetupPlotCoord(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, + progpath, genome, reg2plot, inttag, flanksize, + samprate, galaxy) +attach(plotvar.list) + +# Setup data points for plot. +pts.list <- SetPtsSpline(pint, lgint) +pts <- pts.list$pts # data points for avg. profile and standard errors. +m.pts <- pts.list$m.pts # middle data points. For pint, m.pts=1. +f.pts <- pts.list$f.pts # flanking region data points. + +# Setup matrix for avg. profiles. +regcovMat <- CreatePlotMat(pts, ctg.tbl) +# Setup matrix for standard errors. +confiMat <- CreateConfiMat(se, pts, ctg.tbl) + +# Genomic enrichment for all profiles in the config. Use this for heatmaps. +enrichList <- vector('list', nrow(ctg.tbl)) +cat("Done\n") + +# Load required libraries. +cat("Loading R libraries") +if(!suppressMessages(require(ShortRead, warn.conflicts=F))) { + source("http://bioconductor.org/biocLite.R") + biocLite(ShortRead) + if(!suppressMessages(require(ShortRead, warn.conflicts=F))) { + stop('Loading package ShortRead failed!') + } +} +cat('.') +if(!suppressMessages(require(BSgenome, warn.conflicts=F))) { + source("http://bioconductor.org/biocLite.R") + biocLite(BSgenome) + if(!suppressMessages(require(BSgenome, warn.conflicts=F))) { + stop('Loading package BSgenome failed!') + } +} +cat('.') +if(!suppressMessages(require(doMC, warn.conflicts=F))) { + install.packages('doMC') + if(!suppressMessages(require(doMC, warn.conflicts=F))) { + stop('Loading package doMC failed!') + } +} +# Register doMC with CPU number. +if(cores.number == 0){ + registerDoMC() +} else { + registerDoMC(cores.number) +} +cat('.') +if(!suppressMessages(require(caTools, warn.conflicts=F))) { + install.packages('caTools') + if(!suppressMessages(require(caTools, warn.conflicts=F))) { + stop('Loading package caTools failed!') + } +} +cat('.') +if(!suppressMessages(require(utils, warn.conflicts=F))) { + install.packages('utils') + if(!suppressMessages(require(utils, warn.conflicts=F))) { + stop('Loading package utils failed!') + } +} +cat('.') +cat("Done\n") + +####################################################################### +# Here start to extract coverages for all genomic regions and calculate +# data for plotting. + +cat("Analyze bam files and calculate coverage") +# Extract bam file names from configuration and determine if bam-pair is used. +bfl.res <- bamFileList(ctg.tbl) +bam.pair <- bfl.res$bbp # boolean for bam-pair. +bam.list <- bfl.res$bam.list # bam file list. +CheckHMColorConfig(hm.color, bam.pair) + +# Determine if bowtie is used to generate the bam files. +# Index bam files if not done yet. +v.map.bowtie <- headerIndexBam(bam.list) + +# Retrieve chromosome names for each bam file. +sn.list <- seqnamesBam(bam.list) + +# Calculate library size from bam files for normalization. +v.lib.size <- libSizeBam(bam.list) + +v.low.cutoff <- vector("integer", nrow(ctg.tbl)) # low count cutoffs. +# Process the config file row by row. +# browser() +for(r in 1:nrow(ctg.tbl)) { # r: index of plots/profiles. + + reg <- ctg.tbl$glist[r] # retrieve gene list names. + # Create coordinate chunk indices. + chkidx.list <- chunkIndex(nrow(coord.list[[reg]]), gcs) + + # Do coverage for each bam file. + bam.files <- unlist(strsplit(ctg.tbl$cov[r], ':')) + + # Obtain fraglen for each bam file. + fraglens <- as.integer(unlist(strsplit(ctg.tbl$fraglen[r], ':'))) + + # Obtain bam file basic info. + libsize <- v.lib.size[bam.files[1]] + v.low.cutoff[r] <- low.count / libsize * 1e6 + result.pseudo.rpm <- 1e6 / libsize + sn.inbam <- sn.list[[bam.files[1]]] + # chr.tag <- chrTag(sn.inbam) + chr.tag <- NA # do NOT modify the chromosome names. + is.bowtie <- v.map.bowtie[bam.files[1]] + cat("\nreport reg2plot\n") + cat(reg2plot) + cat("\n") + result.matrix <- covMatrix(debug, chkidx.list, coord.list[[reg]], rnaseq.gb, + exonmodel, libsize, TRUE, chr.tag, pint, + reg2plot, flanksize, flankfactor, m.pts, f.pts, + bufsize, cov.algo, bam.files[1], sn.inbam, + fraglens[1], map.qual, is.bowtie, + strand.spec=strand.spec) + # Rprof(NULL) + if(bam.pair) { # calculate background. + fraglen2 <- ifelse(length(fraglens) > 1, fraglens[2], fraglens[1]) + libsize <- v.lib.size[bam.files[2]] + bkg.pseudo.rpm <- 1e6 / libsize + sn.inbam <- sn.list[[bam.files[2]]] + # chr.tag <- chrTag(sn.inbam) + chr.tag <- NA + is.bowtie <- v.map.bowtie[bam.files[2]] + # if(class(chr.tag) == 'character') { + # stop(sprintf("Read %s error: %s", bam.files[2], chr.tag)) + # } + bkg.matrix <- covMatrix(debug, chkidx.list, coord.list[[reg]], rnaseq.gb, + exonmodel, libsize, TRUE, chr.tag, pint, + reg2plot, flanksize, flankfactor, m.pts, f.pts, + bufsize, cov.algo, bam.files[2], sn.inbam, + fraglen2, map.qual, is.bowtie, + strand.spec=strand.spec) + # browser() + result.matrix <- log2((result.matrix + result.pseudo.rpm) / + (bkg.matrix + bkg.pseudo.rpm)) + } + + # Calculate SEM if needed. Shut off SEM in single gene case. + if(nrow(result.matrix) > 1 && se){ + confiMat[, r] <- apply(result.matrix, 2, function(x) CalcSem(x, robust)) + } + + # Book-keep this matrix for heatmap. + enrichList[[r]] <- result.matrix + + # Return avg. profile. + regcovMat[, r] <- apply(result.matrix, 2, function(x) mean(x, trim=robust, + na.rm=T)) +} +# browser() +cat("Done\n") + +######################################## +# Add row names to heatmap data. +for(i in 1:length(enrichList)) { + reg <- ctg.tbl$glist[i] # gene list name. + rownames(enrichList[[i]]) <- paste(coord.list[[reg]]$gname, + coord.list[[reg]]$tid, sep=':') +} +# Some basic parameters. +xticks <- genXticks(reg2plot, pint, lgint, pts, flanksize, flankfactor, Labs) +unit.width <- 4 +ng.list <- sapply(enrichList, nrow) # number of genes per heatmap. + +# Create image file and plot data into it. +if(!fi_tag){ + cat("Plotting figures...") + #### Average profile plot. #### + out.plot <- avgname + pdf(out.plot, width=plot.width, height=plot.height, pointsize=font.size) + plotmat(regcovMat, ctg.tbl$title, ctg.tbl$color, bam.pair, xticks, pts, + m.pts, f.pts, pint, shade.alp, confiMat, mw, prof.misc) + out.dev <- dev.off() + + #### Heatmap. #### + # Setup output device. + hd <- SetupHeatmapDevice(reg.list, uniq.reg, ng.list, pts, font.size, + unit.width, rr) + reg.hei <- hd$reg.hei # list of image heights for unique regions. + hm.width <- hd$hm.width # image width. + hm.height <- hd$hm.height # image height. + lay.mat <- hd$lay.mat # matrix for heatmap layout. + heatmap.mar <- hd$heatmap.mar # heatmap margins in inches. + + out.hm <- heatmapname + pdf(out.hm, width=hm.width, height=hm.height, pointsize=font.size) + par(mai=heatmap.mar) + layout(lay.mat, heights=reg.hei) + + # Do heatmap plotting. + go.list <- plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, + go.paras, ctg.tbl$title, bam.pair, xticks, flood.frac, + do.plot=T, hm.color=hm.color, color.distr=color.distr, + color.scale=color.scale) + out.dev <- dev.off() + cat("Done\n") +} else { + go.list <- plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, + go.paras, ctg.tbl$title, bam.pair, xticks, flood.frac, + do.plot=F, hm.color=hm.color, color.distr=color.distr, + color.scale=color.scale) +} + +# Save plotting data. +oname1="data" +cat("Saving results...") +dir.create(oname1, showWarnings=F) + +# Average profiles. +out.prof <- file.path(oname1, 'avgprof.txt') +write.table(regcovMat, file=out.prof, row.names=F, sep="\t", quote=F) + +# Standard errors of mean. +if(!is.null(confiMat)){ + out.confi <- file.path(oname1, 'sem.txt') + write.table(confiMat, file=out.confi, row.names=F, sep="\t", quote=F) +} + +# Heatmap density values. +for(i in 1:length(enrichList)) { + reg <- ctg.tbl$glist[i] # gene list name. + out.heat <- file.path(oname1, paste('hm', i, '.txt', sep='')) + write.table(cbind(coord.list[[reg]][, c('gid', 'gname', 'tid', 'strand')], + enrichList[[i]]), + file=out.heat, row.names=F, sep="\t", quote=F) +} + +# Avg. profile R data. +prof.dat <- file.path(oname1, 'avgprof.RData') +save(plot.width, plot.height, regcovMat, ctg.tbl, bam.pair, xticks, pts, + m.pts, f.pts, pint, shade.alp, confiMat, mw, prof.misc, se, v.lib.size, + font.size, + file=prof.dat) + +# Heatmap R data. +heat.dat <- file.path(oname1, 'heatmap.RData') +save(reg.list, uniq.reg, ng.list, pts, enrichList, v.low.cutoff, go.algo, + ctg.tbl, bam.pair, xticks, flood.frac, hm.color, unit.width, rr, + go.list, color.scale, v.lib.size, font.size, go.paras, low.count, + color.distr, + file=heat.dat) +cat("Done\n") + +# Wrap results up. +cat("Wrapping results up...") +cur.dir <- getwd() +out.dir <- dirname(oname1) +out.zip <- basename(oname1) +setwd(out.dir) +if(!zip(paste(out.zip, '.zip', sep=''), out.zip, extras='-q')) { + if(unlink(oname, recursive=T)) { + warning(sprintf("Unable to delete intermediate result folder: %s", + oname)) + } +} +setwd(cur.dir) +cat("Done\n") +cat("All done. Cheers!\n") +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngsplot.xml Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,3185 @@ +<tool id="ngsplot" name="ngsplot" version="0.1.0"> + <description>visualize NGS samples at functional genomic regions - beta</description> + <requirements> + <requirement type="package" version="1.17.1=r3.3.2_1">r-catools</requirement> + <requirement type="package" version="1.3.4">r-domc</requirement> + <requirement type="package" version="1.42.0">bioconductor-bsgenome</requirement> +<!-- <requirement type="package" version="1.26.1">bioconductor-rsamtools</requirement> --> + <requirement type="package" version="1.32.0">bioconductor-shortread</requirement> +<!-- <requirement type="package" version="0.16.1=r3.2.2_0">bioconductor-biocgenerics</requirement> --> + </requirements> + + <command><![CDATA[ +export NGSPLOT="$__tool_directory__" && +#if $numsamples.numsamples2 == "1": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "2": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "3": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "4": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "5": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $numsamples.usepair.bamfile5 + $numsamples.usepair.reffile5 + $numsamples.usepair.genelist5.usegenelist5 + $numsamples.usepair.genelist5.genelist5 + $numsamples.usepair.title5 + $numsamples.usepair.fraglen5 + $numsamples.usepair.linecol5 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "6": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $numsamples.usepair.bamfile5 + $numsamples.usepair.reffile5 + $numsamples.usepair.genelist5.usegenelist5 + $numsamples.usepair.genelist5.genelist5 + $numsamples.usepair.title5 + $numsamples.usepair.fraglen5 + $numsamples.usepair.linecol5 + + $numsamples.usepair.bamfile6 + $numsamples.usepair.reffile6 + $numsamples.usepair.genelist6.usegenelist6 + $numsamples.usepair.genelist6.genelist6 + $numsamples.usepair.title6 + $numsamples.usepair.fraglen6 + $numsamples.usepair.linecol6 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "7": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $numsamples.usepair.bamfile5 + $numsamples.usepair.reffile5 + $numsamples.usepair.genelist5.usegenelist5 + $numsamples.usepair.genelist5.genelist5 + $numsamples.usepair.title5 + $numsamples.usepair.fraglen5 + $numsamples.usepair.linecol5 + + $numsamples.usepair.bamfile6 + $numsamples.usepair.reffile6 + $numsamples.usepair.genelist6.usegenelist6 + $numsamples.usepair.genelist6.genelist6 + $numsamples.usepair.title6 + $numsamples.usepair.fraglen6 + $numsamples.usepair.linecol6 + + $numsamples.usepair.bamfile7 + $numsamples.usepair.reffile7 + $numsamples.usepair.genelist7.usegenelist7 + $numsamples.usepair.genelist7.genelist7 + $numsamples.usepair.title7 + $numsamples.usepair.fraglen7 + $numsamples.usepair.linecol7 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "8": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $numsamples.usepair.bamfile5 + $numsamples.usepair.reffile5 + $numsamples.usepair.genelist5.usegenelist5 + $numsamples.usepair.genelist5.genelist5 + $numsamples.usepair.title5 + $numsamples.usepair.fraglen5 + $numsamples.usepair.linecol5 + + $numsamples.usepair.bamfile6 + $numsamples.usepair.reffile6 + $numsamples.usepair.genelist6.usegenelist6 + $numsamples.usepair.genelist6.genelist6 + $numsamples.usepair.title6 + $numsamples.usepair.fraglen6 + $numsamples.usepair.linecol6 + + $numsamples.usepair.bamfile7 + $numsamples.usepair.reffile7 + $numsamples.usepair.genelist7.usegenelist7 + $numsamples.usepair.genelist7.genelist7 + $numsamples.usepair.title7 + $numsamples.usepair.fraglen7 + $numsamples.usepair.linecol7 + + $numsamples.usepair.bamfile8 + $numsamples.usepair.reffile8 + $numsamples.usepair.genelist8.usegenelist8 + $numsamples.usepair.genelist8.genelist8 + $numsamples.usepair.title8 + $numsamples.usepair.fraglen8 + $numsamples.usepair.linecol8 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "9": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $numsamples.usepair.bamfile5 + $numsamples.usepair.reffile5 + $numsamples.usepair.genelist5.usegenelist5 + $numsamples.usepair.genelist5.genelist5 + $numsamples.usepair.title5 + $numsamples.usepair.fraglen5 + $numsamples.usepair.linecol5 + + $numsamples.usepair.bamfile6 + $numsamples.usepair.reffile6 + $numsamples.usepair.genelist6.usegenelist6 + $numsamples.usepair.genelist6.genelist6 + $numsamples.usepair.title6 + $numsamples.usepair.fraglen6 + $numsamples.usepair.linecol6 + + $numsamples.usepair.bamfile7 + $numsamples.usepair.reffile7 + $numsamples.usepair.genelist7.usegenelist7 + $numsamples.usepair.genelist7.genelist7 + $numsamples.usepair.title7 + $numsamples.usepair.fraglen7 + $numsamples.usepair.linecol7 + + $numsamples.usepair.bamfile8 + $numsamples.usepair.reffile8 + $numsamples.usepair.genelist8.usegenelist8 + $numsamples.usepair.genelist8.genelist8 + $numsamples.usepair.title8 + $numsamples.usepair.fraglen8 + $numsamples.usepair.linecol8 + + $numsamples.usepair.bamfile9 + $numsamples.usepair.reffile9 + $numsamples.usepair.genelist9.usegenelist9 + $numsamples.usepair.genelist9.genelist9 + $numsamples.usepair.title9 + $numsamples.usepair.fraglen9 + $numsamples.usepair.linecol9 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#else if $numsamples.numsamples2 == "10": + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + $numsamples.numsamples2 + $numsamples.usepair.usepair1 + + $numsamples.usepair.bamfile1 + $numsamples.usepair.reffile1 + $numsamples.usepair.genelist1.usegenelist1 + $numsamples.usepair.genelist1.genelist1 + $numsamples.usepair.title1 + $numsamples.usepair.fraglen1 + $numsamples.usepair.linecol1 + + $numsamples.usepair.bamfile2 + $numsamples.usepair.reffile2 + $numsamples.usepair.genelist2.usegenelist2 + $numsamples.usepair.genelist2.genelist2 + $numsamples.usepair.title2 + $numsamples.usepair.fraglen2 + $numsamples.usepair.linecol2 + + $numsamples.usepair.bamfile3 + $numsamples.usepair.reffile3 + $numsamples.usepair.genelist3.usegenelist3 + $numsamples.usepair.genelist3.genelist3 + $numsamples.usepair.title3 + $numsamples.usepair.fraglen3 + $numsamples.usepair.linecol3 + + $numsamples.usepair.bamfile4 + $numsamples.usepair.reffile4 + $numsamples.usepair.genelist4.usegenelist4 + $numsamples.usepair.genelist4.genelist4 + $numsamples.usepair.title4 + $numsamples.usepair.fraglen4 + $numsamples.usepair.linecol4 + + $numsamples.usepair.bamfile5 + $numsamples.usepair.reffile5 + $numsamples.usepair.genelist5.usegenelist5 + $numsamples.usepair.genelist5.genelist5 + $numsamples.usepair.title5 + $numsamples.usepair.fraglen5 + $numsamples.usepair.linecol5 + + $numsamples.usepair.bamfile6 + $numsamples.usepair.reffile6 + $numsamples.usepair.genelist6.usegenelist6 + $numsamples.usepair.genelist6.genelist6 + $numsamples.usepair.title6 + $numsamples.usepair.fraglen6 + $numsamples.usepair.linecol6 + + $numsamples.usepair.bamfile7 + $numsamples.usepair.reffile7 + $numsamples.usepair.genelist7.usegenelist7 + $numsamples.usepair.genelist7.genelist7 + $numsamples.usepair.title7 + $numsamples.usepair.fraglen7 + $numsamples.usepair.linecol7 + + $numsamples.usepair.bamfile8 + $numsamples.usepair.reffile8 + $numsamples.usepair.genelist8.usegenelist8 + $numsamples.usepair.genelist8.genelist8 + $numsamples.usepair.title8 + $numsamples.usepair.fraglen8 + $numsamples.usepair.linecol8 + + $numsamples.usepair.bamfile9 + $numsamples.usepair.reffile9 + $numsamples.usepair.genelist9.usegenelist9 + $numsamples.usepair.genelist9.genelist9 + $numsamples.usepair.title9 + $numsamples.usepair.fraglen9 + $numsamples.usepair.linecol9 + + $numsamples.usepair.bamfile10 + $numsamples.usepair.reffile10 + $numsamples.usepair.genelist10.usegenelist10 + $numsamples.usepair.genelist10.genelist10 + $numsamples.usepair.title10 + $numsamples.usepair.fraglen10 + $numsamples.usepair.linecol10 + + $gene_database + $randomly_sample + $GO.gene_order + $GO.KNC + $GO.MIT + $GO.NRS + $chunk_size + $quality_requirement + $standard_error + $radius_size + $flooding_fraction + $smooth_method + $shaded_area + $out_zip $out_avg_png $out_hm_png + +#end if + + ]]></command> + +<!--> +<--> + +<inputs> + <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" > + </param> + <conditional name="genomic_region_source_type"> + <param type="select" name="genomic_region" label="Genomic region" help=""> + <option value="tss">TSS</option> + <option value="tes">TES</option> + <option value="genebody">Genebody</option> + <option value="exon">Exon</option> + <option value="cgi">CGI</option> + <option value="bed">Customized bed file</option> + </param> + + <when value="tss"> + <param type="select" name="further_information" label="Further information: Not required for TSS"> + <option value="na">Not Required</option> + </param> + <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS"> + <option value="na">Not Required</option> + </param> + <conditional name="flanking_region_option_source_type"> + <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> + <option value="flanking_region_size">Specify flanking region size in base pairs</option> + <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option--> + </param> + <when value="flanking_region_size"> + <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> + </when> + <!--when value="flanking_floating_size"> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + </when--> + </conditional> + </when> + <when value="tes"> + <param type="select" name="further_information" label="Further information: Not required for TES"> + <option value="na">Not Required</option> + </param> + <param name="interval_size" type="select" label="Interval Region Size: Not required for TES"> + <option value="na">Not Required</option> + </param> + <conditional name="flanking_region_option_source_type"> + <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> + <option value="flanking_region_size">Specify flanking region size in base pairs</option> + <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option--> + </param> + <when value="flanking_region_size"> + <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> + </when> + <!--when value="flanking_floating_size"> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + </when--> + </conditional> + </when> + <when value="genebody"> + <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot"> + <option value="chipseq">ChIP-seq</option> + <option value="rnaseq">RNA-seq</option> + </param> + <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> + <option value="automatic">Default</option> + <option value="0">Small</option> + <option value="1">Large</option> + </param> + <conditional name="flanking_region_option_source_type"> + <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> + <option value="flanking_region_size">Specify flanking region size in base pairs</option> + <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> + </param> + <when value="flanking_region_size"> + <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> + </when> + <when value="flanking_floating_size"> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + </when> + </conditional> + </when> + <when value="exon"> + <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot"> + <option value="canonical">Canonical</option> + <option value="variant">Variant</option> + <option value="promoter">Promoter</option> + <option value="polyA">polyA</option> + <option value="altAcceptor">altAcceptor</option> + <option value="altDonor">altDonor</option> + <option value="altBoth">altBoth</option> + </param> + <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> + <option value="automatic">Default</option> + <option value="0">Small</option> + <option value="1">Large</option> + </param> + <conditional name="flanking_region_option_source_type"> + <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> + <option value="flanking_region_size">Specify flanking region size in base pairs</option> + <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> + </param> + <when value="flanking_region_size"> + <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> + </when> + <when value="flanking_floating_size"> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + </when> + </conditional> + </when> + <when value="cgi"> + <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot"> + <option value="ProximalPromoter">ProximalPromoter</option> + <option value="Genebody">GeneBody</option> + <option value="Genedesert">GeneDesert</option> + <option value="OtherIntergenic">OtherIntergenic</option> + <option value="Pericentromere">Pericentromere</option> + <option value="Subtelomere">Subtelomere</option> + <option value="Promoter1k">Promoter1k</option> + <option value="Promoter3k">Promoter3k</option> + </param> + <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> + <option value="automatic">Default</option> + <option value="0">Small</option> + <option value="1">Large</option> + </param> + <conditional name="flanking_region_option_source_type"> + <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> + <option value="flanking_region_size">Specify flanking region size in base pairs</option> + <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> + </param> + <when value="flanking_region_size"> + <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> + </when> + <when value="flanking_floating_size"> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + </when> + </conditional> + </when> + <when value="bed"> + <param type="select" name="further_information" label="Further information: Not required for bed input"> + <option value="na">Not Required</option> + </param> + <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> + <option value="automatic">Default</option> + <option value="0">Small</option> + <option value="1">Large</option> + </param> + <conditional name="flanking_region_option_source_type"> + <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> + <option value="flanking_region_size">Specify flanking region size in base pairs</option> + <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> + </param> + <when value="flanking_region_size"> + <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> + </when> + <when value="flanking_floating_size"> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + </when> + </conditional> + </when> + </conditional> + + + <conditional name="numsamples"> + <param type="select" name="numsamples2" label="Number of samples to plot"> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + <option value="10">10</option> + </param> + + <when value="1"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 1 sample, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 1 sample, no refpairs, entry 1--> + </when> + <when value="yes"> + <!-- START: 1 sample, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 1 sample, yes refpairs, entry 1--> + </when> + </conditional> + </when> + <when value="2"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 2 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 2 samples, no refpairs, entry 1--> + <!-- START: 2 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 2 samples, no refpairs, entry 2--> + </when> + <when value="yes"> + <!-- START: 2 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 2 samples, yes refpairs, entry 1--> + <!-- START: 2 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 2 samples, yes refpairs, entry 2--> + </when> + </conditional> + </when> + <when value="3"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 3 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 3 samples, no refpairs, entry 1--> + <!-- START: 3 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 3 samples, no refpairs, entry 2--> + <!-- START: 3 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 3 samples, no refpairs, entry 3--> + </when> + <when value="yes"> + <!-- START: 3 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 3 samples, yes refpairs, entry 1--> + <!-- START: 3 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 3 samples, yes refpairs, entry 2--> + <!-- START: 3 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 3 samples, yes refpairs, entry 2--> + </when> + </conditional> + </when> + <when value="4"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 4 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 4 samples, no refpairs, entry 1--> + <!-- START: 4 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 4 samples, no refpairs, entry 2--> + <!-- START: 4 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 4 samples, no refpairs, entry 3--> + <!-- START: 4 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 4 samples, no refpairs, entry 4--> + </when> + <when value="yes"> + <!-- START: 4 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 4 samples, yes refpairs, entry 1--> + <!-- START: 4 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 4 samples, yes refpairs, entry 2--> + <!-- START: 4 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 4 samples, yes refpairs, entry 3--> + <!-- START: 4 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 4 samples, yes refpairs, entry 4--> + </when> + </conditional> + </when> + <when value="5"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 5 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 5 samples, no refpairs, entry 1--> + <!-- START: 5 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 5 samples, no refpairs, entry 2--> + <!-- START: 5 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 5 samples, no refpairs, entry 3--> + <!-- START: 5 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 5 samples, no refpairs, entry 4--> + <!-- START: 5 samples, no refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="hidden" name="reffile5" value="na"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 5 samples, no refpairs, entry 5--> + </when> + <when value="yes"> + <!-- START: 5 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 5 samples, yes refpairs, entry 1--> + <!-- START: 5 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 5 samples, yes refpairs, entry 2--> + <!-- START: 5 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 5 samples, yes refpairs, entry 3--> + <!-- START: 5 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 5 samples, yes refpairs, entry 4--> + <!-- START: 5 samples, yes refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 5 samples, yes refpairs, entry 5--> + </when> + </conditional> + </when> + <when value="6"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 6 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 6 samples, no refpairs, entry 1--> + <!-- START: 6 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 6 samples, no refpairs, entry 2--> + <!-- START: 6 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 6 samples, no refpairs, entry 3--> + <!-- START: 6 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 6 samples, no refpairs, entry 4--> + <!-- START: 6 samples, no refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="hidden" name="reffile5" value="na"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 6 samples, no refpairs, entry 5--> + <!-- START: 6 samples, no refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="hidden" name="reffile6" value="na"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 6 samples, no refpairs, entry 6--> + </when> + <when value="yes"> + <!-- START: 6 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 6 samples, yes refpairs, entry 1--> + <!-- START: 6 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 6 samples, yes refpairs, entry 2--> + <!-- START: 6 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 6 samples, yes refpairs, entry 3--> + <!-- START: 6 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 6 samples, yes refpairs, entry 4--> + <!-- START: 6 samples, yes refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 6 samples, yes refpairs, entry 5--> + <!-- START: 6 samples, yes refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 6 samples, yes refpairs, entry 6--> + </when> + </conditional> + </when> + <when value="7"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 7 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 1--> + <!-- START: 7 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 2--> + <!-- START: 7 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 3--> + <!-- START: 7 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 4--> + <!-- START: 7 samples, no refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="hidden" name="reffile5" value="na"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 5--> + <!-- START: 7 samples, no refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="hidden" name="reffile6" value="na"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 6--> + <!-- START: 7 samples, no refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="hidden" name="reffile7" value="na"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 7 samples, no refpairs, entry 7--> + </when> + <when value="yes"> + <!-- START: 7 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 1--> + <!-- START: 7 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 2--> + <!-- START: 7 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 3--> + <!-- START: 7 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 4--> + <!-- START: 7 samples, yes refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 5--> + <!-- START: 7 samples, yes refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 6--> + <!-- START: 7 samples, yes refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 7 samples, yes refpairs, entry 7--> + </when> + </conditional> + </when> + <when value="8"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 8 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 1--> + <!-- START: 8 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 2--> + <!-- START: 8 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 3--> + <!-- START: 8 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 4--> + <!-- START: 8 samples, no refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="hidden" name="reffile5" value="na"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 5--> + <!-- START: 8 samples, no refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="hidden" name="reffile6" value="na"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 6--> + <!-- START: 8 samples, no refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="hidden" name="reffile7" value="na"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 7--> + <!-- START: 8 samples, no refpairs, entry 8--> + <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> + <param type="hidden" name="reffile8" value="na"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist8" label="Sample 8: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist8" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> + <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> + <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> + <!-- END: 8 samples, no refpairs, entry 8--> + </when> + <when value="yes"> + <!-- START: 8 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 1--> + <!-- START: 8 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 2--> + <!-- START: 8 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 3--> + <!-- START: 8 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 4--> + <!-- START: 8 samples, yes refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 5--> + <!-- START: 8 samples, yes refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 6--> + <!-- START: 8 samples, yes refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 7--> + <!-- START: 8 samples, yes refpairs, entry 8--> + <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> + <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/> + <conditional name="genelist8"> + <param type="select" name="usegenelist8" label="Sample 8: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist8" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> + <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> + <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> + <!-- END: 8 samples, yes refpairs, entry 8--> + </when> + </conditional> + </when> + <when value="9"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 9 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 1--> + <!-- START: 9 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 2--> + <!-- START: 9 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 3--> + <!-- START: 9 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 4--> + <!-- START: 9 samples, no refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="hidden" name="reffile5" value="na"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 5--> + <!-- START: 9 samples, no refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="hidden" name="reffile6" value="na"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 6--> + <!-- START: 9 samples, no refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="hidden" name="reffile7" value="na"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 7--> + <!-- START: 9 samples, no refpairs, entry 8--> + <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> + <param type="hidden" name="reffile8" value="na"/> + <conditional name="genelist8"> + <param type="select" name="usegenelist8" label="Sample 8: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist8" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> + <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> + <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 8--> + <!-- START: 9 samples, no refpairs, entry 9--> + <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> + <param type="hidden" name="reffile9" value="na"/> + <conditional name="genelist9"> + <param type="select" name="usegenelist9" label="Sample 9: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist9" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> + <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> + <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> + <!-- END: 9 samples, no refpairs, entry 9--> + </when> + <when value="yes"> + <!-- START: 9 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 1--> + <!-- START: 9 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 2--> + <!-- START: 9 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 3--> + <!-- START: 9 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 4--> + <!-- START: 9 samples, yes refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 5--> + <!-- START: 9 samples, yes refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 6--> + <!-- START: 9 samples, yes refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 7--> + <!-- START: 9 samples, yes refpairs, entry 8--> + <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> + <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/> + <conditional name="genelist8"> + <param type="select" name="usegenelist8" label="Sample 8: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist8" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> + <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> + <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 8--> + <!-- START: 9 samples, yes refpairs, entry 9--> + <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> + <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/> + <conditional name="genelist9"> + <param type="select" name="usegenelist9" label="Sample 9: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist9" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> + <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> + <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> + <!-- END: 9 samples, yes refpairs, entry 9--> + </when> + </conditional> + </when> + <when value="10"> + <conditional name="usepair"> + <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- START: 10 samples, no refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="hidden" name="reffile1" value="na"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 1--> + <!-- START: 10 samples, no refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="hidden" name="reffile2" value="na"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 2--> + <!-- START: 10 samples, no refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="hidden" name="reffile3" value="na"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 3--> + <!-- START: 10 samples, no refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="hidden" name="reffile4" value="na"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 4--> + <!-- START: 10 samples, no refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="hidden" name="reffile5" value="na"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 5--> + <!-- START: 10 samples, no refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="hidden" name="reffile6" value="na"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 6--> + <!-- START: 10 samples, no refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="hidden" name="reffile7" value="na"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 7--> + <!-- START: 10 samples, no refpairs, entry 8--> + <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> + <param type="hidden" name="reffile8" value="na"/> + <conditional name="genelist8"> + <param type="select" name="usegenelist8" label="Sample 8: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist8" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> + <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> + <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 8--> + <!-- START: 10 samples, no refpairs, entry 9--> + <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> + <param type="hidden" name="reffile9" value="na"/> + <conditional name="genelist9"> + <param type="select" name="usegenelist9" label="Sample 9: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist9" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> + <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> + <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 9--> + <!-- START: 10 samples, no refpairs, entry 10--> + <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/> + <param type="hidden" name="reffile10" value="na"/> + <conditional name="genelist10"> + <param type="select" name="usegenelist10" label="Sample 10: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist10" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/> + <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/> + <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/> + <!-- END: 10 samples, no refpairs, entry 10--> + </when> + <when value="yes"> + <!-- START: 10 samples, yes refpairs, entry 1--> + <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <conditional name="genelist1"> + <param type="select" name="usegenelist1" label="Sample 1: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist1" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 1--> + <!-- START: 10 samples, yes refpairs, entry 2--> + <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> + <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> + <conditional name="genelist2"> + <param type="select" name="usegenelist2" label="Sample 2: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist2" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> + <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> + <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 2--> + <!-- START: 10 samples, yes refpairs, entry 3--> + <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> + <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> + <conditional name="genelist3"> + <param type="select" name="usegenelist3" label="Sample 3: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist3" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> + <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> + <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 3--> + <!-- START: 10 samples, yes refpairs, entry 4--> + <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> + <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> + <conditional name="genelist4"> + <param type="select" name="usegenelist4" label="Sample 4: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist4" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> + <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> + <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 4--> + <!-- START: 10 samples, yes refpairs, entry 5--> + <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> + <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> + <conditional name="genelist5"> + <param type="select" name="usegenelist5" label="Sample 5: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist5" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> + <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> + <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 5--> + <!-- START: 10 samples, yes refpairs, entry 6--> + <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> + <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> + <conditional name="genelist6"> + <param type="select" name="usegenelist6" label="Sample 6: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist6" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> + <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> + <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 6--> + <!-- START: 10 samples, yes refpairs, entry 7--> + <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> + <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> + <conditional name="genelist7"> + <param type="select" name="usegenelist7" label="Sample 7: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist7" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> + <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> + <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 7--> + <!-- START: 10 samples, yes refpairs, entry 8--> + <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> + <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/> + <conditional name="genelist8"> + <param type="select" name="usegenelist8" label="Sample 8: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist8" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> + <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> + <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 8--> + <!-- START: 10 samples, yes refpairs, entry 9--> + <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> + <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/> + <conditional name="genelist9"> + <param type="select" name="usegenelist9" label="Sample 9: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist9" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> + <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> + <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 9--> + <!-- START: 10 samples, yes refpairs, entry 10--> + <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/> + <param type="data" name="reffile10" label="Sample 10: Reference BAM file"/> + <conditional name="genelist10"> + <param type="select" name="usegenelist10" label="Sample 10: Gene list"> + <option value="no">Plot whole genome</option> + <option value="yes">Provide restricted gene list</option> + </param> + <when value="no"> + <param type="hidden" name="genelist10" value="-1"/> + </when> + <when value="yes"> + <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/> + </when> + </conditional> + <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/> + <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/> + <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/> + <!-- END: 10 samples, yes refpairs, entry 10--> + </when> + </conditional> + </when> + </conditional> + + + + <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl"> + <option value="ensembl">Ensembl</option> + <option value="refseq">RefSeq</option> + </param> + <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/> + <conditional name="GO"> + <param type="select" name="gene_order" label="Gene order algorithm"> + <option value="total">Overall enrichment of the 1st profile</option> + <option value="hc">Hierarchical clustering</option> + <option value="max">Peak value of the 1st profile</option> + <option value="prod">Product of all profiles on the same region</option> + <option value="diff">Difference between the 1st and 2nd profiles</option> + <option value="km">K-means clustering</option> + <option value="none">No ranking algorithm applied. Use order in gene list.</option> + </param> + <when value="km"> + <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/> + <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/> + <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="total"> + <param type="hidden" name="KNC" value="NA" /> + <param type="hidden" name="MIT" value="NA" /> + <param type="hidden" name="NRS" value="NA" /> + </when> + <when value="hc"> + <param type="hidden" name="KNC" value="NA" /> + <param type="hidden" name="MIT" value="NA" /> + <param type="hidden" name="NRS" value="NA" /> + </when> + <when value="max"> + <param type="hidden" name="KNC" value="NA" /> + <param type="hidden" name="MIT" value="NA" /> + <param type="hidden" name="NRS" value="NA" /> + </when> + <when value="prod"> + <param type="hidden" name="KNC" value="NA" /> + <param type="hidden" name="MIT" value="NA" /> + <param type="hidden" name="NRS" value="NA" /> + </when> + <when value="diff"> + <param type="hidden" name="KNC" value="NA" /> + <param type="hidden" name="MIT" value="NA" /> + <param type="hidden" name="NRS" value="NA" /> + </when> + <when value="none"> + <param type="hidden" name="KNC" value="NA" /> + <param type="hidden" name="MIT" value="NA" /> + <param type="hidden" name="NRS" value="NA" /> + </when> + </conditional> + <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/> + <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/> + <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve."> + <option value="1">Yes</option> + <option value="0">No</option> + </param> + + <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/> + <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/> + <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles"> + <option value="1">No</option> + <option value="3">Slightly</option> + <option value="5">Somewhat</option> + <option value="9">Quite</option> + <option value="13">Super</option> + </param> + <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/> +<!-- +--> +</inputs> + +<help></help> +<outputs> + <data format="pdf" name="out_avg_png" /> + <data format="pdf" name="out_hm_png" /> + <data format="zip" name="out_zip"/> +</outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/replot.xml.notworking Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,157 @@ +<tool id="replot" name="replot"> +<command interpreter="perl"> +#if $outtype.outtype2 == "prof": + runreplot.pl $input_zipfile $outtype.outtype2 $output_filename + $outtype.WD + $outtype.HG + $outtype.SE + $outtype.H + $outtype.MW + $outtype.Y.Y2 + $outtype.Y.Y3 + $outtype.LEG + $outtype.BOX + $outtype.VLN + $outtype.XYL + $outtype.LWD + $outtype.FS +#else if $outtype.outtype2 == "heatmap": + runreplot.pl $input_zipfile $outtype.outtype2 $output_filename + $outtype.GO.GO2 + $outtype.GO.KNC + $outtype.GO.MIT + $outtype.GO.NRS + $outtype.LOW + $outtype.RR + $outtype.FC + $outtype.CO + $outtype.CD + $outtype.FS + dummy + dummy + dummy +#end if: + +</command> + +<!--> + + +<--> + +<inputs> + <param type="data" name="input_zipfile" multiple="false" label="Input zip file created by ngsplot"/> + + <conditional name="outtype"> + <param type="select" name="outtype2" label="Select figure type to replot"> + <option value="prof">Coverage Profile</option> + <option value="heatmap">Heatmap</option> + </param> + + <when value="prof"> + <param type="text" name="WD" value="8" label="Image width in inches" /> + <param type="text" name="HG" value="7" label="Image height in inches" /> + <param type="select" name="SE" label="Standard error shading" > + <option value="1">Yes, include standard error shading</option> + <option value="0">No, exclude standard error shading</option> + </param> + <param type="text" name="H" value="0" label="Opacity of shaded area under each curve" help="Use 0 for no shading. Suggested value of between 0 and 0.5 will add a semi-transparent shade under each curve."/> + <param type="text" name="MW" value="1" label="Moving window width to smooth average profiles" help="The unit of the window size is a data point. In ngs.plot, the number of data points on the X-axis is 100. A moving window width of 10 means averaging over 10% of the entire X-axis."/> + <conditional name="Y"> + <param type="select" name="Y2" label="Define Y-axis scale?" > + <option value="no">No, let program decide</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param type="text" name="Y3" value="0,100" label="Y-axis min_val,max_val" help="Enter minimum and maximum value separated by comma" /> + </when> + <when value="no"> + <param type="hidden" name="Y3" value="na" label="test"/> + </when> + </conditional> + <param type="select" name="LEG" label="Draw legend?" > + <option value="1">Yes</option> + <option value="0">No</option> + </param> + <param type="select" name="BOX" label="Draw box around plot?" > + <option value="1">Yes</option> + <option value="0">No</option> + </param> + <param type="select" name="VLN" label="Draw vertical lines?" > + <option value="1">Yes</option> + <option value="0">No</option> + </param> + <param type="select" name="XYL" label="Draw axis labels?" > + <option value="1">Yes</option> + <option value="0">No</option> + </param> + <param type="text" name="LWD" value="3" label="Line width" /> + <param type="text" name="FS" value="12" label="Font size" /> +<!--> +<--> + + </when> + <when value="heatmap"> + <conditional name="GO"> + <param type="select" name="GO2" label="Gene order algorithm" > + <option value="total">Overall enrichment of the 1st profile (default)</option> + <option value="hc">Hierarchial clustering</option> + <option value="max">Peak value of the 1st profile</option> + <option value="prod">Product of all profiles on the same region</option> + <option value="diff">Difference between 1st and 2nd profiles</option> + <option value="km">K-means clustering.</option> + <option value="none">No ranking algorithm applied, use order in gene list.</option> + </param> + <when value="km"> + <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/> + <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/> + <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="total"> + <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/> + <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/> + <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="hc"> + <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/> + <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/> + <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="max"> + <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/> + <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/> + <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="prod"> + <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/> + <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/> + <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="diff"> + <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/> + <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/> + <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + <when value="none"> + <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/> + <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/> + <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> + </when> + </conditional> + <param type="text" name="LOW" value="10" label="Low count cutoff in rank-based normalization" help="This number is in raw read counts."/> + <param type="text" name="RR" value="30" label="Reduce ratio" help="This controls the heatmap height. The smaller the value, the taller the heatmap." /> + <param type="text" name="FC" value="0.02" label="Flooding fraction" help="The default value of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic." /> + <param type="text" name="CO" value="default" label="Color for heatmap" help="For non bam-pair plots, input a single color. For bam-pair plots, use color-tri format (neg_color:[neu_color]:pos_color). Hint: must use R colors, such as darkgreen, yellow and blue2. The neutral color is optional(default=black)." /> + <param type="text" name="CD" value="0.6" label="Color distribution for heatmap" help="Must be a positive number. Hint: lower values give more widely spaced colors at the negative end. In other words, they shift the neutral color to positive values. If set to 1, the neutral color represents 0(i.e. no bias). If set to >1, the neutral color represents a negative value." /> + <param type="text" name="FS" value="12" label="Font size" /> + </when> + </conditional> +<!-- +--> +</inputs> + +<help></help> +<outputs> + <data format="pdf" name="output_filename" /> +</outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runNGSplot.pl Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,129 @@ +#!/usr/bin/perl -w +use strict; +use File::Basename 'dirname'; +use File::Spec; +use Cwd 'abs_path'; + +my @inputs = @ARGV; +my @inputs2 = @inputs; + +my $genome_name = shift(@inputs); +my $genomic_region_source_type__genomic_region = shift(@inputs); +my $genomic_region_source_type__further_information = shift(@inputs); +my $genomic_region_source_type__interval_size = shift(@inputs); +my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_option = shift(@inputs); +my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size = shift(@inputs); +my $numsamples = shift(@inputs); +my $usepairs = shift(@inputs); + +#print STDERR "inputs @inputs\n"; + +my $randfile = rand(100)."\.config\.txt"; +my $randfile2 = $randfile; +$randfile2 =~ s/config\.txt/logfile/gm; + +my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile"); +open(FILE,">$outfile"); + +for (my $i=1;$i<=$numsamples;$i++) { + my $bamfile=shift(@inputs); + my $reffile=shift(@inputs); + my $usegenelist=shift(@inputs); + my $genelist=shift(@inputs); + my $title=shift(@inputs); + my $fraglen=shift(@inputs); + my $color=shift(@inputs); + if ($usepairs eq 'yes') { + syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n"); + }else { + syswrite(FILE, "$bamfile\t$genelist\t$title\t$fraglen\t$color\n"); + } +} +close(FILE); + +my $gene_database = shift(@inputs); +my $randomly_sample = shift(@inputs); +my $gene_order = shift(@inputs); +my $knc = shift(@inputs); +my $mit = shift(@inputs); +my $nrs = shift(@inputs); +my $chunk_size = shift(@inputs); +my $quality_requirement = shift(@inputs); +my $standard_error = shift(@inputs); +my $radius_size = shift(@inputs); +my $flooding_fraction = shift(@inputs); +my $smooth_method = shift(@inputs); +my $shaded_area = shift(@inputs); +my $out_name = shift(@inputs); +my $out_avg_name = shift(@inputs); +my $out_hm_name = shift(@inputs); + + +my $G = $genome_name; +my $R = $genomic_region_source_type__genomic_region; +my $C = $outfile; +my $O = $out_name; +my $O2 = $out_avg_name; +my $O3 = $out_hm_name; +my $F = $genomic_region_source_type__further_information; +my $D = $gene_database; +my $L = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size; +my $N = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size; +my $RB = $radius_size; +my $S = $randomly_sample; +my $CS = $chunk_size; +my $MQ = $quality_requirement; +my $IN = $genomic_region_source_type__interval_size; +my $SE = $standard_error; +my $MW = $smooth_method; +my $H = $shaded_area; +my $GO = $gene_order; +my $KNC = $knc; +my $MIT = $mit; +my $NRS = $nrs; +my $FC = $flooding_fraction; + +if ($GO eq 'km') { + $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS"; +} + +my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2"); +open(FILE2,">>$logfile"); +my $cmd5="pwd >> $logfile 2>&1"; +system($cmd5); +my $NGSPLOT = $ENV{"NGSPLOT"}; +my $cmd=''; +if (($R eq 'tss')||($R eq 'tes')) { + $cmd = "Rscript $NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; +}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') { + if ($IN eq 'automatic') { + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; + }else { + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; + } +}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') { + if ($IN eq 'automatic') { + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; + }else { + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; + } +} + +print("$cmd\n"); +my $cmd2="cp data.zip $O"; +my $cmd3="rm $outfile"; +my $cmd4="rm $logfile"; +syswrite(FILE2, "\n$cmd\n"); +syswrite(FILE2, "\n$cmd2\n"); +syswrite(FILE2, "\n$cmd3\n"); +syswrite(FILE2, "\n$cmd4\n\n"); + +# print STDERR "cmd: $cmd\n"; +system($cmd); +system($cmd2); +#system($cmd3); +#system($cmd4); + +close(FILE2); + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runreplot.pl Wed Dec 06 19:01:53 2017 -0500 @@ -0,0 +1,63 @@ +#!/usr/bin/perl -w +use strict; +use File::Basename 'dirname'; +use File::Spec; +use Cwd 'abs_path'; + +my $input_file = $ARGV[0]; +my $output_type = $ARGV[1]; +my $output_filename = $ARGV[2]; + +my $cmd1 = "cp $input_file data.zip"; +my $cmd2 = ""; +my $cmd3 = "mv output.pdf $output_filename"; + +my $FS = ""; +if ($output_type eq 'prof') { + my $WD = "-WD $ARGV[3]"; + my $HG = "-HG $ARGV[4]"; + my $SE = "-SE $ARGV[5]"; + my $H = "-H $ARGV[6]"; + my $MW = "-MW $ARGV[7]"; + my $Y = "-Y $ARGV[8]"; + my $YAS = "-YAS $ARGV[9]"; + my $LEG = "-LEG $ARGV[10]"; + my $BOX = "-BOX $ARGV[11]"; + my $VLN = "-VLN $ARGV[12]"; + my $XYL = "-XYL $ARGV[13]"; + my $LWD = "-LWD $ARGV[14]"; + $FS = "-FS $ARGV[15]"; + + if ($Y =~ /no$/gm) { + $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS"; + }else { + $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS $YAS"; + } +}elsif ($output_type eq 'heatmap') { + my $GO = "-GO $ARGV[3]"; + my $KNC = "-KNC $ARGV[4]"; + my $MIT = "-MIT $ARGV[5]"; + my $NRS = "-NRS $ARGV[6]"; + my $LOW = "-LOW $ARGV[7]"; + my $RR = "-RR $ARGV[8]"; + my $FC = "-FC $ARGV[9]"; + my $CO = "-CO $ARGV[10]"; + my $CD = "-CD $ARGV[11]"; + $FS = "-FS $ARGV[12]"; + my $DUM1 = $ARGV[13]; + my $DUM2 = $ARGV[14]; + my $DUM3 = $ARGV[15]; + + if ($CO =~ /default/gm) { $CO = ""; } + + if ($GO =~ /km$/gm) { + $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO $KNC $MIT $NRS"; + }else { + $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO"; + } +} +system($cmd1); +system($cmd2); +system($cmd3); + +