# HG changeset patch
# User artbio
# Date 1503926987 14400
# Node ID a35e6f9c1d34a391e2fe921c1722e85efeed11e2

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6719543c5017d581ae012b864d7c9088f0767fc8

diff -r 000000000000 -r a35e6f9c1d34 signature.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature.py	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,209 @@
+import argparse
+from collections import defaultdict
+
+import numpy
+
+import pysam
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument(
+        '--input', action="store", type=str, help="bam alignment file")
+    the_parser.add_argument(
+        '--minquery', type=int,
+        help="Minimum readsize of query reads (nt) - must be an integer")
+    the_parser.add_argument(
+        '--maxquery', type=int,
+        help="Maximum readsize of query reads (nt) - must be an integer")
+    the_parser.add_argument(
+        '--mintarget', type=int,
+        help="Minimum readsize of target reads (nt) - must be an integer")
+    the_parser.add_argument(
+        '--maxtarget', type=int,
+        help="Maximum readsize of target reads (nt) - must be an integer")
+    the_parser.add_argument(
+        '--minscope', type=int,
+        help="Minimum overlap analyzed (nt) - must be an integer")
+    the_parser.add_argument(
+        '--maxscope', type=int,
+        help="Maximum overlap analyzed (nt) - must be an integer")
+    the_parser.add_argument(
+        '--output_h', action="store", type=str,
+        help="h-signature dataframe")
+    the_parser.add_argument(
+        '--output_z', action="store", type=str,
+        help="z-signature dataframe")
+    args = the_parser.parse_args()
+    return args
+
+
+class Map:
+
+    def __init__(self, bam_file):
+        self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
+        self.chromosomes = dict(zip(self.bam_object.references,
+                                self.bam_object.lengths))
+        self.map_dict = self.create_map(self.bam_object)
+
+    def create_map(self, bam_object):
+        '''
+        Returns a map_dictionary {(chromosome,read_position,polarity):
+                                                    [read_length, ...]}
+        '''
+        map_dictionary = defaultdict(list)
+        # get empty value for start and end of each chromosome
+        for chrom in self.chromosomes:
+            map_dictionary[(chrom, 1, 'F')] = []
+            map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
+        for chrom in self.chromosomes:
+            for read in bam_object.fetch(chrom):
+                positions = read.positions  # a list of covered positions
+                if read.is_reverse:
+                    map_dictionary[(chrom, positions[-1]+1,
+                                    'R')].append(read.query_alignment_length)
+                else:
+                    map_dictionary[(chrom, positions[0]+1,
+                                    'F')].append(read.query_alignment_length)
+        return map_dictionary
+
+    def signature_tables(self, minquery, maxquery, mintarget, maxtarget):
+        query_range = range(minquery, maxquery + 1)
+        target_range = range(mintarget, maxtarget + 1)
+        Query_table = defaultdict(dict)
+        Target_table = defaultdict(dict)
+        for key in self.map_dict:
+            for size in self.map_dict[key]:
+                if size in query_range or size in target_range:
+                    if key[2] == 'F':
+                        coordinate = key[1]
+                    else:
+                        coordinate = -key[1]
+                if size in query_range:
+                    Query_table[key[0]][coordinate] = Query_table[key[0]].get(
+                        coordinate, 0) + 1
+                if size in target_range:
+                    Target_table[key[0]][coordinate] = \
+                        Target_table[key[0]].get(coordinate, 0) + 1
+        return Query_table, Target_table
+
+    def compute_signature_z(self, minquery, maxquery, mintarget, maxtarget,
+                            scope, zscore="no"):
+        Query_table, Target_table = self.signature_tables(minquery, maxquery,
+                                                     mintarget, maxtarget)
+        frequency_table = defaultdict(dict)
+        for chrom in self.chromosomes:
+            for overlap in scope:
+                frequency_table[chrom][overlap] = 0
+        for chrom in Query_table:
+            for coord in Query_table[chrom]:
+                for overlap in scope:
+                    frequency_table[chrom][overlap] += min(
+                        Query_table[chrom][coord],
+                        Target_table[chrom].get(-coord - overlap + 1, 0))
+        # since we want the number of pairs, not the number or paired reads
+        # to do: what in complex cases
+        # with query and target sizes partially overlap ?
+        for chrom in frequency_table:
+            for overlap in frequency_table[chrom]:
+                frequency_table[chrom][overlap] /= 2
+        # compute overlaps for all chromosomes merged
+        for overlap in scope:
+            accumulator = []
+            for chrom in frequency_table:
+                if chrom != 'all_chromosomes':
+                    accumulator.append(frequency_table[chrom][overlap])
+            frequency_table['all_chromosomes'][overlap] = sum(accumulator)
+        return self.stringify_table(frequency_table)
+
+    def compute_signature_h(self, minquery, maxquery, mintarget,
+                                   maxtarget, scope):
+        Query_table, Target_table = self.signature_tables(minquery, maxquery,
+                                                     mintarget, maxtarget)
+        frequency_table = defaultdict(dict)
+        for chrom in self.chromosomes:
+            for overlap in scope:
+                frequency_table[chrom][overlap] = 0
+        for chrom in Query_table:
+            Total_Query_Numb = 0
+            for coord in Query_table[chrom]:
+                Total_Query_Numb += Query_table[chrom][coord]
+            for coord in Query_table[chrom]:
+                local_table = dict([(overlap, 0) for overlap in scope])
+                number_of_targets = 0
+                for overlap in scope:
+                    local_table[overlap] += Query_table[chrom][coord] * \
+                        Target_table[chrom].get(-coord - overlap + 1, 0)
+                    number_of_targets += Target_table[chrom].get(
+                        -coord - overlap + 1, 0)
+                for overlap in scope:
+                    try:
+                        frequency_table[chrom][overlap] += \
+                            local_table[overlap] / number_of_targets \
+                            / float(Total_Query_Numb)
+                    except ZeroDivisionError:
+                        continue
+        # compute overlap probabilities for all chromosomes merged
+        general_frequency_table = dict([(overlap, 0) for overlap in scope])
+        total_aligned_reads = 0
+        for chrom in frequency_table:
+            for overlap in frequency_table[chrom]:
+                total_aligned_reads += self.bam_object.count(chrom)
+        for chrom in frequency_table:
+            for overlap in frequency_table[chrom]:
+                try:
+                    general_frequency_table[overlap] += \
+                        frequency_table[chrom][overlap] / total_aligned_reads \
+                        * self.bam_object.count(chrom)
+                except ZeroDivisionError:
+                    continue
+        for overlap in general_frequency_table:
+            frequency_table['all_chromosomes'][overlap] = \
+                general_frequency_table[overlap]
+        return self.stringify_table(frequency_table)
+
+    def stringify_table(self, frequency_table):
+        '''
+        method both to compute z-score and to return a writable string
+        '''
+        tablestring = []
+        for chrom in sorted(frequency_table):
+            accumulator = []
+            for overlap in frequency_table[chrom]:
+                accumulator.append(frequency_table[chrom][overlap])
+            z_mean = numpy.mean(accumulator)
+            z_std = numpy.std(accumulator)
+            if z_std == 0:
+                for overlap in sorted(frequency_table[chrom]):
+                    tablestring.append('%s\t%s\t%s\t%s\n' % (
+                        chrom, str(overlap),
+                        str(frequency_table[chrom][overlap]), str(0)))
+            else:
+                for overlap in sorted(frequency_table[chrom]):
+                    tablestring.append('%s\t%s\t%s\t%s\n' % (
+                        chrom, str(overlap),
+                        str(frequency_table[chrom][overlap]),
+                        str((frequency_table[chrom][overlap] - z_mean)/z_std)))
+        return ''.join(tablestring)
+
+
+
+def main(input, minquery, maxquery, mintarget, maxtarget, minscope, maxscope,
+         output_h, output_z, genome_wide=False, zscore="no"):
+    H = open(output_h, 'w')
+    Z = open(output_z, 'w')
+    mapobj = Map(input)
+    scope = range(minscope, maxscope + 1)
+    Z.write(mapobj.compute_signature_z(minquery, maxquery, mintarget,
+            maxtarget, scope, zscore="no"))
+    H.write(mapobj.compute_signature_h(minquery, maxquery, mintarget,
+            maxtarget, scope))
+    H.close()
+    Z.close()
+
+
+if __name__ == "__main__":
+    args = Parser()
+    main(args.input, args.minquery, args.maxquery, args.mintarget,
+         args.maxtarget, args.minscope, args.maxscope, args.output_h,
+         args.output_z)
diff -r 000000000000 -r a35e6f9c1d34 signature.r
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature.r	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,99 @@
+## Setup R error handling to go to stderr
+#options(show.error.messages=F,
+        #error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+warnings()
+
+library(RColorBrewer)
+library(lattice)
+library(latticeExtra)
+library(grid)
+library(gridExtra)
+library(optparse)
+
+option_list <- list(
+    make_option("--h_dataframe", type="character", help="path to h-signature dataframe"),
+    make_option("--z_dataframe", type="character", help="path to z-signature dataframe"),
+    make_option("--plot_method", type = "character", help="How  data should be plotted (global or lattice)"),
+    make_option("--pdf", type = "character", help="path to the pdf file with plots"),
+    make_option("--title", type = "character", help="Graph Title")
+    )
+ 
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args = parse_args(parser)
+
+
+
+ 
+# data frames implementation
+h_dataframe = read.delim(args$h_dataframe, header=F)
+colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score")
+h_dataframe$sig = h_dataframe$sig * 100  # to get probs in %
+z_dataframe = read.delim(args$z_dataframe, header=F)
+colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score")
+
+# functions
+      globalgraph = function () {
+        pdf(args$pdf)
+        par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
+        
+        plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,3)],
+             type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)",
+             ylab="Numbers of pairs", col="darkslateblue", lwd=4)
+
+        plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,4)],
+             type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)",
+             ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2)
+
+        plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,3)],
+             type = "l", main="Overlap probabilities", cex.main=1, xlab="overlap (nt)",
+             ylab="Probability [%]", ylim=c(0,50), pch=19, col="darkslateblue", lwd=2)
+
+        plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)],
+             type = "l", main="Overlap Probability Z-scores", cex.main=1,
+             xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2,
+             col="darkslateblue", lwd=2)
+
+        mtext(args$title, outer = TRUE, cex=1)
+        dev.off()
+      }
+
+      treillisgraph = function (df, ...) {
+          pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677
+          p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df,
+                   type = "l",
+                   col='darkblue',
+                   cex=0.5,
+                   scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)),
+                   xlab = "Overlap",
+                   ylab = "signature (Nbr of pairs / Overlap prob.)",
+                   main = args$title,
+                   par.strip.text=list(cex=.5),
+                   pch=19, lwd =2,
+                   as.table=TRUE,
+                   layout=c(2,12),
+                   newpage = T,
+                   ...)
+           plot(p) 
+           dev.off()
+      }
+
+# main
+
+if (args$plot_method=="global") {
+    globalgraph()
+    }
+
+if(args$plot_method=="lattice") {
+    # rearrange dataframes
+    h_sig = h_dataframe[,c(1,2,3)]
+    h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig)
+    colnames(h_sig) = c("method", "chrom", "overlap", "sig")
+    z_pairs = z_dataframe[,c(1,2,3)]
+    z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs)
+    colnames(z_pairs) = c("method", "chrom", "overlap", "sig")
+    lattice_df = rbind(z_pairs, h_sig)
+    par.settings.treillis=list(strip.background = list(
+            col = c("lightblue", "lightgreen")))
+
+    treillisgraph(lattice_df, par.settings=par.settings.treillis)    
+}
diff -r 000000000000 -r a35e6f9c1d34 signature.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature.xml	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,119 @@
+<tool id="signature" name="Small RNA Signatures" version="3.0.0">
+    <description />
+    <requirements>
+        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
+        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
+        <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
+        <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement>
+        <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+      <command detect_errors="exit_code"><![CDATA[
+        samtools index '$input' &&
+        python '$__tool_directory__'/signature.py
+           --input '$input'
+           --minquery '$minquery'
+           --maxquery '$maxquery'
+           --mintarget '$mintarget'
+           --maxtarget '$maxtarget'
+           --minscope '$minscope'
+           --maxscope '$maxscope'
+           --output_h '$h_dataframe'
+           --output_z '$z_dataframe' &&
+        Rscript '$__tool_directory__'/signature.r
+           --h_dataframe '$h_dataframe'
+           --z_dataframe '$z_dataframe'
+           --plot_method '$plot_method'
+           --pdf '$pdf'
+           --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
+    ]]></command>
+    <inputs>
+        <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
+        <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
+        <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
+        <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
+        <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
+        <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
+        <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
+        <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select">
+            <option selected="True" value="global">Global</option>
+            <option value="lattice">Lattice</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="z-signature data frame" name="z_dataframe">
+            <actions>
+                <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />
+            </actions>
+        </data>
+        <data format="tabular" label="h-signature data frame" name="h_dataframe">
+            <actions>
+                <action name="column_names" type="metadata" default="Chromosome,Overlap,overlap_probability,z-score" />
+            </actions>
+        </data>
+        <data format="pdf" label="Overlap probabilities" name="pdf" />
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="bam" name="input" value="sr_bowtie.bam" />
+            <param name="minquery" value="23" />
+            <param name="maxquery" value="29" />
+            <param name="mintarget" value="23" />
+            <param name="maxtarget" value="29" />
+            <param name="minscope" value="5" />
+            <param name="maxscope" value="15" />
+            <param name="plot_method" value="global" />
+            <output file="h.tab" ftype="tabular" name="h_dataframe" />
+            <output file="z.tab" ftype="tabular" name="z_dataframe" />
+            <output file="global.pdf" ftype="pdf" name="pdf" />
+        </test>
+        <test>
+            <param ftype="bam" name="input" value="sr_bowtie.bam" />
+            <param name="minquery" value="23" />
+            <param name="maxquery" value="29" />
+            <param name="mintarget" value="23" />
+            <param name="maxtarget" value="29" />
+            <param name="minscope" value="5" />
+            <param name="maxscope" value="15" />
+            <param name="plot_method" value="lattice" />
+            <output file="h.tab" ftype="tabular" name="h_dataframe" />
+            <output file="z.tab" ftype="tabular" name="z_dataframe" />
+            <output file="lattice.pdf" ftype="pdf" name="pdf" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Compute small RNA (piRNA, siRNA, ...) signatures.
+
+This tool computes (i) the number of pairs by overlap classes (in nt) and associated the z-scores,
+and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. 
+Options set the min and max size of both the query small rna class and the target small rna class, 
+the range over which to compute the signatures, and whether the signatures should be reported at 
+genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 
+for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
+
+.. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
+.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
+
+**Input**
+
+A **sorted** BAM alignment file.
+
+**Outputs**
+
+**Global**: The number of pairs founds, the ping-pong signal and the associated z-scores 
+are computed at genome-wide level and returned in a pdf file.
+
+**Lattice**: The number of pairs founds, the ping-pong signals and the associated z-scores 
+are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.
+
+
+        </help>
+    <citations>
+            <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r a35e6f9c1d34 test-data/global.pdf
Binary file test-data/global.pdf has changed
diff -r 000000000000 -r a35e6f9c1d34 test-data/h.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/h.tab	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,1331 @@
+FBgn0000004_17.6	5	0.0	-0.565685424949
+FBgn0000004_17.6	6	0.0	-0.565685424949
+FBgn0000004_17.6	7	0.00369003690037	0.989949493661
+FBgn0000004_17.6	8	0.0	-0.565685424949
+FBgn0000004_17.6	9	0.0	-0.565685424949
+FBgn0000004_17.6	10	0.00369003690037	0.989949493661
+FBgn0000004_17.6	11	0.0	-0.565685424949
+FBgn0000004_17.6	12	0.0	-0.565685424949
+FBgn0000004_17.6	13	0.0	-0.565685424949
+FBgn0000004_17.6	14	0.0	-0.565685424949
+FBgn0000004_17.6	15	0.00738007380074	2.54558441227
+FBgn0000005_297	5	0	0
+FBgn0000005_297	6	0	0
+FBgn0000005_297	7	0	0
+FBgn0000005_297	8	0	0
+FBgn0000005_297	9	0	0
+FBgn0000005_297	10	0	0
+FBgn0000005_297	11	0	0
+FBgn0000005_297	12	0	0
+FBgn0000005_297	13	0	0
+FBgn0000005_297	14	0	0
+FBgn0000005_297	15	0	0
+FBgn0000006_412	5	0.0	-0.876714007519
+FBgn0000006_412	6	0.00186046511628	-0.187867287326
+FBgn0000006_412	7	0.00279069767442	0.156556072771
+FBgn0000006_412	8	0.0	-0.876714007519
+FBgn0000006_412	9	0.0046511627907	0.845402792965
+FBgn0000006_412	10	0.00837209302326	2.22309623335
+FBgn0000006_412	11	0.00279069767442	0.156556072771
+FBgn0000006_412	12	0.0	-0.876714007519
+FBgn0000006_412	13	0.00558139534884	1.18982615306
+FBgn0000006_412	14	0.0	-0.876714007519
+FBgn0000006_412	15	0.0	-0.876714007519
+FBgn0000007_1731	5	0.0	-0.383239046572
+FBgn0000007_1731	6	0.0	-0.383239046572
+FBgn0000007_1731	7	0.0	-0.383239046572
+FBgn0000007_1731	8	0.0	-0.383239046572
+FBgn0000007_1731	9	0.0	-0.383239046572
+FBgn0000007_1731	10	0.0017667844523	-0.149037407
+FBgn0000007_1731	11	0.0265017667845	3.12978554701
+FBgn0000007_1731	12	0.0	-0.383239046572
+FBgn0000007_1731	13	0.0	-0.383239046572
+FBgn0000007_1731	14	0.00353356890459	0.0851642325717
+FBgn0000007_1731	15	0.0	-0.383239046572
+FBgn0000155_roo	5	0.0	-0.849506616033
+FBgn0000155_roo	6	0.00292153589316	-0.39207997663
+FBgn0000155_roo	7	0.000834724540902	-0.718813290489
+FBgn0000155_roo	8	0.00333889816361	-0.326733313859
+FBgn0000155_roo	9	0.0016694490818	-0.588119964946
+FBgn0000155_roo	10	0.0200333889816	2.28713319701
+FBgn0000155_roo	11	0.00667779632721	0.196039988315
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diff -r 000000000000 -r a35e6f9c1d34 test-data/lattice.pdf
Binary file test-data/lattice.pdf has changed
diff -r 000000000000 -r a35e6f9c1d34 test-data/sr_bowtie.bam
Binary file test-data/sr_bowtie.bam has changed
diff -r 000000000000 -r a35e6f9c1d34 test-data/z.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/z.tab	Mon Aug 28 09:29:47 2017 -0400
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+FBgn0067405_R1-2	11	0	0
+FBgn0067405_R1-2	12	0	0
+FBgn0067405_R1-2	13	0	0
+FBgn0067405_R1-2	14	0	0
+FBgn0067405_R1-2	15	0	0
+FBgn0067418_Helitron	5	0	0
+FBgn0067418_Helitron	6	0	0
+FBgn0067418_Helitron	7	0	0
+FBgn0067418_Helitron	8	0	0
+FBgn0067418_Helitron	9	0	0
+FBgn0067418_Helitron	10	0	0
+FBgn0067418_Helitron	11	0	0
+FBgn0067418_Helitron	12	0	0
+FBgn0067418_Helitron	13	0	0
+FBgn0067418_Helitron	14	0	0
+FBgn0067418_Helitron	15	0	0
+FBgn0067419_G7	5	0	0
+FBgn0067419_G7	6	0	0
+FBgn0067419_G7	7	0	0
+FBgn0067419_G7	8	0	0
+FBgn0067419_G7	9	0	0
+FBgn0067419_G7	10	0	0
+FBgn0067419_G7	11	0	0
+FBgn0067419_G7	12	0	0
+FBgn0067419_G7	13	0	0
+FBgn0067419_G7	14	0	0
+FBgn0067419_G7	15	0	0
+FBgn0067420_Fw3	5	0	0
+FBgn0067420_Fw3	6	0	0
+FBgn0067420_Fw3	7	0	0
+FBgn0067420_Fw3	8	0	0
+FBgn0067420_Fw3	9	0	0
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+FBgn0067420_Fw3	11	0	0
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+FBgn0067420_Fw3	13	0	0
+FBgn0067420_Fw3	14	0	0
+FBgn0067420_Fw3	15	0	0
+FBgn0067421_Fw2	5	0	0
+FBgn0067421_Fw2	6	0	0
+FBgn0067421_Fw2	7	0	0
+FBgn0067421_Fw2	8	0	0
+FBgn0067421_Fw2	9	0	0
+FBgn0067421_Fw2	10	0	0
+FBgn0067421_Fw2	11	0	0
+FBgn0067421_Fw2	12	0	0
+FBgn0067421_Fw2	13	0	0
+FBgn0067421_Fw2	14	0	0
+FBgn0067421_Fw2	15	0	0
+FBgn0067624_BS3	5	0	-0.316227766017
+FBgn0067624_BS3	6	0	-0.316227766017
+FBgn0067624_BS3	7	0	-0.316227766017
+FBgn0067624_BS3	8	0	-0.316227766017
+FBgn0067624_BS3	9	0	-0.316227766017
+FBgn0067624_BS3	10	3	3.16227766017
+FBgn0067624_BS3	11	0	-0.316227766017
+FBgn0067624_BS3	12	0	-0.316227766017
+FBgn0067624_BS3	13	0	-0.316227766017
+FBgn0067624_BS3	14	0	-0.316227766017
+FBgn0067624_BS3	15	0	-0.316227766017
+FBgn0067624_BS4	5	0	0
+FBgn0067624_BS4	6	0	0
+FBgn0067624_BS4	7	0	0
+FBgn0067624_BS4	8	0	0
+FBgn0067624_BS4	9	0	0
+FBgn0067624_BS4	10	0	0
+FBgn0067624_BS4	11	0	0
+FBgn0067624_BS4	12	0	0
+FBgn0067624_BS4	13	0	0
+FBgn0067624_BS4	14	0	0
+FBgn0067624_BS4	15	0	0
+FBgn0069340_Tc1-2	5	0	-0.316227766017
+FBgn0069340_Tc1-2	6	0	-0.316227766017
+FBgn0069340_Tc1-2	7	0	-0.316227766017
+FBgn0069340_Tc1-2	8	1	3.16227766017
+FBgn0069340_Tc1-2	9	0	-0.316227766017
+FBgn0069340_Tc1-2	10	0	-0.316227766017
+FBgn0069340_Tc1-2	11	0	-0.316227766017
+FBgn0069340_Tc1-2	12	0	-0.316227766017
+FBgn0069340_Tc1-2	13	0	-0.316227766017
+FBgn0069340_Tc1-2	14	0	-0.316227766017
+FBgn0069340_Tc1-2	15	0	-0.316227766017
+FBgn0069433_G5A	5	0	0
+FBgn0069433_G5A	6	0	0
+FBgn0069433_G5A	7	0	0
+FBgn0069433_G5A	8	0	0
+FBgn0069433_G5A	9	0	0
+FBgn0069433_G5A	10	0	0
+FBgn0069433_G5A	11	0	0
+FBgn0069433_G5A	12	0	0
+FBgn0069433_G5A	13	0	0
+FBgn0069433_G5A	14	0	0
+FBgn0069433_G5A	15	0	0
+FBgn0069587_Doc4-element	5	0	0
+FBgn0069587_Doc4-element	6	0	0
+FBgn0069587_Doc4-element	7	0	0
+FBgn0069587_Doc4-element	8	0	0
+FBgn0069587_Doc4-element	9	0	0
+FBgn0069587_Doc4-element	10	0	0
+FBgn0069587_Doc4-element	11	0	0
+FBgn0069587_Doc4-element	12	0	0
+FBgn0069587_Doc4-element	13	0	0
+FBgn0069587_Doc4-element	14	0	0
+FBgn0069587_Doc4-element	15	0	0
+all_chromosomes	5	2	-1.08978129104
+all_chromosomes	6	43	-0.422900202493
+all_chromosomes	7	44	-0.40663481009
+all_chromosomes	8	60	-0.146388531632
+all_chromosomes	9	71	0.0325307848072
+all_chromosomes	10	254	3.00909759466
+all_chromosomes	11	70	0.0162653924036
+all_chromosomes	12	43	-0.422900202493
+all_chromosomes	13	43	-0.422900202493
+all_chromosomes	14	58	-0.17891931644
+all_chromosomes	15	71	0.0325307848072
diff -r 000000000000 -r a35e6f9c1d34 tool-data/bowtie_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon	 hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full	 hg18	hg18 Full	 /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19	hg19	hg19	 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r a35e6f9c1d34 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie_indices.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r a35e6f9c1d34 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bowtie" version="1.1.2">
+      <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.3">
+      <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biocbasics" version="2.14">
+        <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>