# HG changeset patch
# User devteam
# Date 1377540984 14400
# Node ID a110f9d6ae246b3ffe5a3c73dffdb160342dd3ba

Uploaded tool tarball.

diff -r 000000000000 -r a110f9d6ae24 pileup_interval.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pileup_interval.py	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+
+"""
+Condenses pileup format into ranges of bases.
+
+usage: %prog [options]
+   -i, --input=i: Input pileup file
+   -o, --output=o: Output pileup
+   -c, --coverage=c: Coverage
+   -f, --format=f: Pileup format
+   -b, --base=b: Base to select
+   -s, --seq_column=s: Sequence column
+   -l, --loc_column=l: Base location column
+   -r, --base_column=r: Reference base column
+   -C, --cvrg_column=C: Coverage column
+"""
+
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+import sys
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    strout = ''
+    #Parse Command Line
+    options, args = doc_optparse.parse( __doc__ )
+    coverage = int(options.coverage)
+    fin = file(options.input, 'r')
+    fout = file(options.output, 'w')
+    inLine = fin.readline()
+    if options.format == 'six':
+        seqIndex = 0
+        locIndex = 1
+        baseIndex = 2
+        covIndex = 3
+    elif options.format == 'ten':
+        seqIndex = 0
+        locIndex = 1
+        if options.base == 'first':
+            baseIndex = 2
+        else:
+            baseIndex = 3
+        covIndex = 7
+    else:
+        seqIndex = int(options.seq_column) - 1
+        locIndex = int(options.loc_column) - 1
+        baseIndex = int(options.base_column) - 1
+        covIndex = int(options.cvrg_column) - 1
+    lastSeq = ''
+    lastLoc = -1
+    locs = []
+    startLoc = -1
+    bases = []
+    while inLine.strip() != '':
+        lineParts = inLine.split('\t')
+        try:
+            seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
+        except IndexError, ei:
+            if options.format == 'ten':
+                stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
+            else:
+                stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
+        except ValueError, ev:
+            if options.format == 'six':
+                stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
+            else:
+                stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) )
+#        strout += str(startLoc) + '\n'
+#        strout += str(bases) + '\n'
+#        strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)
+        if loc == lastLoc+1 or lastLoc == -1:
+            if cov >= coverage:
+                if seq == lastSeq or lastSeq == '':
+                    if startLoc == -1:
+                        startLoc = loc
+                    locs.append(loc)
+                    bases.append(base)
+                else:
+                    if len(bases) > 0:
+                        fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+                    startLoc = loc
+                    locs = [loc]
+                    bases = [base]
+            else:
+                if len(bases) > 0:
+                    fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+                startLoc = -1
+                locs = []
+                bases = []
+        else:
+            if len(bases) > 0:
+                fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+            if cov >= coverage:
+                startLoc = loc
+                locs = [loc]
+                bases = [base]
+            else:
+                startLoc = -1
+                locs = []
+                bases = []
+        lastSeq = seq
+        lastLoc = loc
+        inLine = fin.readline()
+    if len(bases) > 0:
+        fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+    fout.close()
+    fin.close()
+    
+#    import sys
+#    strout += file(fout.name,'r').read()
+#    sys.stderr.write(strout)
+
+if __name__ == "__main__" : __main__()
diff -r 000000000000 -r a110f9d6ae24 pileup_interval.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pileup_interval.xml	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,189 @@
+<tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.0">
+  <description>condenses pileup format into ranges of bases</description>
+  <requirements>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <command interpreter="python">
+    pileup_interval.py 
+      --input=$input 
+      --output=$output 
+      --coverage=$coverage
+      --format=$format_type.format
+      #if $format_type.format == "ten":
+       --base=$format_type.which_base
+       --seq_column="None"
+       --loc_column="None"
+       --base_column="None"
+       --cvrg_column="None"
+      #elif $format_type.format == "manual":
+       --base="None"
+       --seq_column=$format_type.seq_column
+       --loc_column=$format_type.loc_column
+       --base_column=$format_type.base_column
+       --cvrg_column=$format_type.cvrg_column
+      #else:
+       --base="None"
+       --seq_column="None"
+       --loc_column="None"
+       --base_column="None"
+       --cvrg_column="None"
+      #end if
+  </command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Choose a pileup file to condense:" />
+    <conditional name="format_type">
+      <param name="format" type="select" label="which contains:" help="See &quot;Types of pileup datasets&quot; below for examples">
+        <option value="six" selected="true">Pileup with six columns (simple)</option>
+        <option value="ten">Pileup with ten columns (with consensus)</option>
+        <option value="manual">Set columns manually</option>
+      </param>
+      <when value="six" />
+      <when value="ten">
+        <param name="which_base" type="select" label="Which base do you want to concatenate">
+          <option value="first" selected="true">Reference base (first)</option>
+          <option value="second">Consensus base (second)</option>
+        </param>
+      </when>
+      <when value="manual">
+        <param name="seq_column" label="Select column with sequence name" type="data_column" numerical="false" data_ref="input" />
+        <param name="loc_column" label="Select column with base location" type="data_column" numerical="false" data_ref="input" />
+        <param name="base_column" label="Select column with base to concatenate" type="data_column" numerical="false" data_ref="input" />
+        <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" />
+      </when>
+    </conditional>
+    <param name="coverage" type="integer" value="3" label="Do not report bases with coverage less than:" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="pileup_interval_in1.tabular" />
+      <param name="format" value="six" />
+      <param name="coverage" value="3" />
+      <output name="output" file="pileup_interval_out1.tabular" />
+    </test>
+    <test>
+      <param name="input" value="pileup_interval_in2.tabular" />
+      <param name="format" value="ten" />
+      <param name="which_base" value="first" />
+      <param name="coverage" value="3" />
+      <output name="output" file="pileup_interval_out2.tabular" />
+    </test>
+    <test>
+      <param name="input" value="pileup_interval_in2.tabular" />
+      <param name="format" value="manual" />
+      <param name="seq_column" value="1" />
+      <param name="loc_column" value="2" />
+      <param name="base_column" value="3" />
+      <param name="cvrg_column" value="8" />
+      <param name="coverage" value="3" />
+      <output name="output" file="pileup_interval_out2.tabular" />
+    </test>
+  </tests> 
+  <help>
+    	
+**What is does**
+
+Reduces the size of a results set by taking a pileup file and producing a condensed version showing consecutive sequences of bases meeting coverage criteria. The tool works on six and ten column pileup formats produced with *samtools pileup* command. You also can specify columns for the input file manually. The tool assumes that the pileup dataset was produced by *samtools pileup* command (although you can override this by setting column assignments manually).
+
+--------
+
+**Types of pileup datasets**
+
+The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below.
+
+.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml
+
+**Six column pileup**::
+
+    1    2  3  4        5        6
+ ---------------------------------   
+ chrM  412  A  2       .,       II
+ chrM  413  G  4     ..t,     IIIH
+ chrM  414  C  4     ...a     III2
+ chrM  415  C  4     TTTt     III7
+   
+where::
+
+ Column Definition
+ ------ ----------------------------
+      1 Chromosome
+      2 Position (1-based)
+      3 Reference base at that position
+      4 Coverage (# reads aligning over that position)
+      5 Bases within reads where (see Galaxy wiki for more info)
+      6 Quality values (phred33 scale, see Galaxy wiki for more)
+       
+**Ten column pileup**
+
+The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command::
+
+
+    1    2  3  4   5   6   7   8       9       10
+ ------------------------------------------------
+ chrM  412  A  A  75   0  25  2       .,       II
+ chrM  413  G  G  72   0  25  4     ..t,     IIIH
+ chrM  414  C  C  75   0  25  4     ...a     III2
+ chrM  415  C  T  75  75  25  4     TTTt     III7
+
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Position (1-based)
+       3 Reference base at that position
+       4 Consensus bases
+       5 Consensus quality
+       6 SNP quality
+       7 Maximum mapping quality
+       8 Coverage (# reads aligning over that position)
+       9 Bases within reads where (see Galaxy wiki for more info)
+      10 Quality values (phred33 scale, see Galaxy wiki for more)
+
+
+.. __: http://samtools.sourceforge.net/cns0.shtml
+
+------
+
+**The output format**
+
+The output file condenses the information in the pileup file so that consecutive bases are listed together as sequences. The starting and ending points of the sequence range are listed, with the starting value converted to a 0-based value. 
+
+Given the following input with minimum coverage set to 3::
+
+    1    2  3  4        5        6
+ ---------------------------------   
+ chr1  112  G  3     ..Ta     III6
+ chr1  113  T  2     aT..     III5
+ chr1  114  A  5     ,,..     IIH2
+ chr1  115  C  4      ,.,      III
+ chrM  412  A  2       .,       II
+ chrM  413  G  4     ..t,     IIIH
+ chrM  414  C  4     ...a     III2
+ chrM  415  C  4     TTTt     III7
+ chrM  490  T  3        a        I
+ 
+the following would be the output::
+ 
+    1    2    3  4
+ -------------------
+ chr1  111  112  G
+ chr1  113  115  AC
+ chrM  412  415  GCC
+ chrM  489  490  T
+
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Starting position (0-based)
+       3 Ending position (1-based)
+       4 Sequence of bases
+ 	
+  </help>
+</tool>
+
+
diff -r 000000000000 -r a110f9d6ae24 test-data/pileup_interval_in1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_interval_in1.tabular	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,118 @@
+chr1	1	G	3	,	3
+chr1	5	A	5	,	I
+chr1	10	T	2	,	I
+chr1	11	C	3	,	I
+chr1	12	G	4	,	I
+chr1	13	C	2	,	I
+chr1	14	A	3	,	I
+chr1	15	T	3	,	6
+chr1	16	A	2	,	3
+chr1	17	T	4	,	I
+chr1	2735	C	3	,	I
+chrM	2736	t	3	,	9
+chrM	2737	t	3	,	I
+chrM	2738	a	3	,	I
+chrM	2739	c	3	,	I
+chrM	2740	a	3	,	I
+chrM	2741	c	3	,	I
+chrM	2742	t	4	,	5
+chrM	2743	c	5	,	I
+chrM	2744	a	2	,	I
+chrM	2745	g	1	,	I
+chrM	2746	a	1	,	I
+chrM	2747	g	1	,	I
+chrM	2748	g	1	,	I
+chrM	2749	t	1	,	I
+chrM	2750	t	1	,	I
+chrM	2751	c	1	,	I
+chrM	2752	a	1	,	I
+chrM	2753	a	1	,	I
+chrM	2754	c	1	,	I
+chrM	2755	t	1	,	I
+chrM	2756	c	1	,	I
+chrM	2757	c	1	,	I
+chrM	2758	t	5	,	I
+chrM	2759	c	3	,	I
+chrM	2760	t	1	,	I
+chrM	2761	c	1	,	I
+chrM	2762	c	1	n	"
+chrM	2763	c	1	n	"
+chrM	2764	t	1	,	I
+chrM	2765	a	1	,	I
+chrM	2766	a	1	,	I
+chrM	2767	c	1	,	I
+chrM	2768	a	1	,	I
+chrM	2769	a	1	,	I
+chrM	2770	c	1	,$	I
+chrM	9563	C	1	^:,	I
+chrM	9564	T	1	,	+
+chrM	9565	G	1	,	-
+chrM	9566	A	1	,	I
+chrM	9567	C	1	,	I
+chrM	9568	T	1	,	?
+chrM	9569	A	1	,	I
+chrM	9570	C	1	,	D
+chrM	9571	C	1	,	I
+chrM	9572	A	1	,	I
+chrM	9573	C	1	,	I
+chrM	9574	A	1	,	I
+chrM	9575	A	1	,	I
+chrM	9576	C	1	,	I
+chrM	9577	T	1	,	I
+chrM	9578	A	1	,	I
+chrM	9579	A	1	,	I
+chrM	9580	A	1	,	I
+chrM	9581	C	1	,	I
+chrM	9582	A	1	,	I
+chrM	9583	T	1	,	I
+chrM	9584	C	1	,	I
+chrM	9585	T	1	,	I
+chrM	9586	A	1	,	I
+chrM	9587	T	1	,	I
+chrM	9588	G	1	,	I
+chrM	9589	C	1	,	I
+chrM	9590	A	1	n	"
+chrM	9591	G	1	n	"
+chrM	9592	A	1	,	I
+chrM	9593	A	1	,	I
+chrM	9594	A	1	,	I
+chrM	9595	A	1	,	I
+chrM	9596	A	1	,	I
+chrM	9597	A	1	,	I
+chrM	9598	C	1	,$	I
+chrM	10864	T	1	^!,	~
+chrM	10865	G	1	,	~
+chrM	10866	T	1	,	~
+chrM	10867	A	1	,	~
+chrM	10868	G	1	,	~
+chrM	10869	A	1	,	~
+chrM	10870	A	1	,	~
+chrM	10871	G	1	,	~
+chrM	10872	C	1	,	~
+chrM	10873	C	3	,	~
+chrM	10874	C	3	,	~
+chrM	10875	C	3	,	~
+chrM	10876	A	3	,	~
+chrM	10877	A	3	,	~
+chrM	10878	T	3	,	~
+chrM	10879	T	3	,	~
+chrM	10880	G	3	,	~
+chrM	10881	C	3	,	~
+chrM	10882	C	3	,	~
+chrM	10883	G	3	,	~
+chrM	10884	G	3	,	~
+chrM	10885	A	1	,	~
+chrM	10886	T	1	,	~
+chrM	10887	C	1	,	~
+chrM	10888	C	1	,	~
+chrM	10889	A	1	,	~
+chrM	10890	T	1	,	~
+chrM	10891	A	1	n	~
+chrM	10892	G	1	n	~
+chrM	10893	T	1	,	~
+chrM	10894	G	1	,	~
+chrM	10895	C	1	,	~
+chrM	10896	T	3	,	~
+chrM	10897	A	3	,	~
+chrM	10898	G	3	,	~
+chrM	10899	C	3	,$	~
diff -r 000000000000 -r a110f9d6ae24 test-data/pileup_interval_in2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_interval_in2.tabular	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,99 @@
+chr1	5016020	t	T	33	0	25	2	..	II
+chr1	5016021	g	G	32	0	25	2	..	)I
+chr1	5016022	t	T	28	0	25	2	..	I$
+chr1	5016023	t	T	33	0	25	2	..	II
+chr1	5016024	t	T	33	0	25	2	..	II
+chr1	5016025	c	C	39	0	25	4	..^:,^:,	II:/
+chr1	5016026	t	T	28	0	25	4	..,c	III$
+chr1	5016027	c	C	39	0	25	4	..,,	H0+7
+chr1	5016028	t	T	28	0	25	4	..,g	III$
+chr1	5016029	g	G	10	0	25	4	T.,t	BII#
+chr1	5016030	c	C	39	0	25	4	.$.$,,	@)6I
+chr1	5016031	t	T	33	0	25	2	,,	IF
+chr1	5016032	t	G	0	0	25	2	,g	IC
+chr1	5016033	c	C	33	0	25	2	,,	1I
+chr1	5016034	t	T	33	0	25	2	,,	II
+chr1	12459316	G	G	7	0	0	2	..	II
+chr1	12459317	G	G	7	0	0	2	..	II
+chr1	12459318	A	A	10	0	0	3	..^!.	III
+chr1	12459319	T	T	10	0	0	3	...	III
+chr1	12459320	C	C	10	0	0	3	...	III
+chr1	12459321	T	T	10	0	0	3	...	III
+chr1	12459322	A	A	10	0	0	3	...	.II
+chr1	12459323	C	C	10	0	0	3	...	?II
+chr1	12459324	A	A	10	0	0	3	...	G?I
+chr1	12459325	C	C	10	0	0	3	...	II;
+chr1	12459326	A	A	10	0	0	3	...	I@B
+chr1	12459327	C	C	10	0	0	3	...	8II
+chr1	12459328	A	A	10	0	0	3	...	IH5
+chr1	12459329	T	T	10	0	0	3	...	I;I
+chr1	12459330	C	C	10	0	0	3	...	IAI
+chr1	12459331	T	T	10	0	0	3	...	3HI
+chr1	49116109	C	C	28	0	18	2	..	G?
+chr1	49116110	A	A	28	0	18	2	..	'@
+chr1	49116111	G	G	26	0	18	2	..	68
+chr1	49116112	A	A	9	0	18	2	..	1'
+chr1	49116113	G	G	20	0	18	2	..	I2
+chr1	49116114	G	G	2	0	20	3	A.^:,	&&$
+chr1	49116115	G	G	21	0	20	3	.A,	8$I
+chr1	49116116	T	T	31	0	20	3	..,	.9%
+chr1	49116117	T	T	36	0	20	3	..,	I55
+chr1	49116118	T	T	36	0	20	3	..,	II+
+chr1	49116119	T	T	36	0	20	3	..,	II8
+chr1	49116120	G	G	32	0	20	3	..,	&%B
+chr1	49116121	T	T	36	0	20	3	.$.,	<63
+chr1	49116122	C	C	33	0	25	2	.,	+I
+chr1	49116123	T	T	33	0	25	2	.,	-7
+chr1	49116124	G	G	29	0	25	2	.,	%I
+chr1	49116125	C	C	24	0	25	2	.$,	+/
+chr1	126866554	G	G	7	0	0	2	..	(I
+chr1	126866555	C	C	10	0	0	3	.$.^!.	III
+chr1	126866556	C	C	7	0	0	2	..	II
+chr11	1021425	C	C	4	0	0	1	.	I
+chr11	1021426	A	A	4	0	0	1	.	I
+chr11	1021427	G	G	4	0	0	1	.	I
+chr11	1021428	G	G	28	0	18	2	.^:.	0I
+chr11	1021429	G	G	19	0	18	2	C.	$I
+chr11	1021430	G	G	36	0	20	3	..^:.	III
+chr11	1021431	T	T	36	0	20	3	...	III
+chr11	1021432	G	G	36	0	20	3	...	III
+chr11	1021433	A	A	36	0	20	3	...	@II
+chr11	1021434	C	C	36	0	20	3	...	%II
+chr11	1021435	G	G	36	0	20	3	...	#II
+chr11	1021436	T	T	36	0	20	3	...	8II
+chr11	1021437	G	G	36	0	20	3	...	/II
+chr11	1021438	G	G	36	0	20	3	...	III
+chr11	1021439	G	G	36	0	20	3	...	;II
+chr11	1021440	C	C	28	0	20	3	N..	"II
+chr11	1021441	T	T	36	0	20	3	...	IFI
+chr11	1021442	G	G	36	0	20	3	...	III
+chr11	1021443	T	T	36	0	20	3	...	III
+chr11	1021444	G	G	28	0	20	3	T..	#II
+chr11	1021445	T	T	28	0	20	3	C..	#II
+chr11	1021446	C	C	36	0	20	3	.$..	:II
+chr11	1021447	T	T	33	0	25	2	..	II
+chr11	1021448	G	G	33	0	25	2	..	II
+chr11	1021449	T	T	33	0	25	2	..	7I
+chr11	1021450	G	G	33	0	25	2	..	II
+chr14	1021451	T	A	33	0	25	3	..	4I
+chr14	80839355	A	A	33	0	25	2	..	I*
+chr14	80839356	G	G	28	0	25	2	..	I#
+chr14	80839357	A	A	31	0	25	2	..	I(
+chr14	80839358	A	A	32	0	25	2	..	I)
+chr14	80839359	T	T	39	0	25	4	..^:,^:,	I+I(
+chr14	80839360	T	T	39	0	25	4	..,,	I+I+
+chr14	80839361	C	C	39	0	25	4	..,,	I&5(
+chr14	80839362	T	T	39	0	25	4	..,,	I3II
+chr14	80839363	G	G	39	0	25	4	..,,	G#I4
+chr14	80839364	G	G	39	0	25	4	..,,	I'II
+chr14	80839365	A	A	39	0	25	4	..,,	@)IH
+chr14	80839366	T	T	39	0	25	4	..,,	I/I2
+chr14	80839367	A	A	39	0	25	4	..,,	I,I=
+chr14	80839368	T	T	39	0	25	4	..,,	I.I7
+chr14	80839369	T	T	39	0	25	4	..,,	I4II
+chr14	80839370	T	T	39	0	25	4	..,,	I2I0
+chr14	80839371	A	A	39	0	25	4	.$.$,,	;+I?
+chr14	80839372	C	C	14	0	25	2	,a	5$
+chr14	80839373	A	A	33	0	25	2	,,	II
+chr14	80839374	T	T	33	0	25	2	,,	II
+chr14	80839375	T	T	33	0	25	2	,,	I?
diff -r 000000000000 -r a110f9d6ae24 test-data/pileup_interval_out1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_interval_out1.tabular	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,10 @@
+chr1	0	1	G
+chr1	4	5	A
+chr1	10	12	CG
+chr1	13	15	AT
+chr1	16	17	T
+chr1	2734	2735	C
+chrM	2735	2743	ttacactc
+chrM	2757	2759	tc
+chrM	10872	10884	CCCAATTGCCGG
+chrM	10895	10899	TAGC
diff -r 000000000000 -r a110f9d6ae24 test-data/pileup_interval_out2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_interval_out2.tabular	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,7 @@
+chr1	5016024	5016030	ctctgc
+chr1	12459317	12459331	ATCTACACACATCT
+chr1	49116113	49116121	GGTTTTGT
+chr1	126866554	126866555	C
+chr11	1021429	1021446	GTGACGTGGGCTGTGTC
+chr14	1021450	1021451	T
+chr14	80839358	80839371	TTCTGGATATTTA
diff -r 000000000000 -r a110f9d6ae24 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 26 14:16:24 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="a7936f4ea405" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>