# HG changeset patch
# User peterjc
# Date 1430319434 14400
# Node ID b7d17d1228d9d932c8af230a8ff5ea24cc1f3892
# Parent 978617e4b6a46fa6d2e4e7e4e4eed8fa3b072aa1
Uploaded v0.0.8, better error handling and relaxed the test
diff -r 978617e4b6a4 -r b7d17d1228d9 test-data/magic.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/magic.pdf Wed Apr 29 10:57:14 2015 -0400
@@ -0,0 +1,1 @@
+%PDF-1.4
diff -r 978617e4b6a4 -r b7d17d1228d9 test-data/venn_list1.pdf
Binary file test-data/venn_list1.pdf has changed
diff -r 978617e4b6a4 -r b7d17d1228d9 tools/plotting/venn_list.py
--- a/tools/plotting/venn_list.py Tue Sep 17 12:02:42 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-#!/usr/bin/env python
-"""Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy)
-
-This script is copyright 2010 by Peter Cock, The James Hutton Institute
-(formerly SCRI), UK. All rights reserved.
-See accompanying text file for licence details (MIT/BSD style).
-
-This is version 0.0.4 of the script.
-"""
-
-
-import sys
-import rpy
-
-def stop_err(msg, error_level=1):
- """Print error message to stdout and quit with given error level."""
- sys.stderr.write("%s\n" % msg)
- sys.exit(error_level)
-
-try:
- import rpy
-except ImportError:
- stop_err("Requires the Python library rpy (to call R)")
-
-try:
- rpy.r.library("limma")
-except:
- stop_err("Requires the R library limma (for vennDiagram function)")
-
-
-if len(sys.argv)-1 not in [7, 10, 13]:
- stop_err("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1))
-
-all_file, all_type, all_label = sys.argv[1:4]
-set_data = []
-if len(sys.argv)-1 >= 7:
- set_data.append(tuple(sys.argv[4:7]))
-if len(sys.argv)-1 >= 10:
- set_data.append(tuple(sys.argv[7:10]))
-if len(sys.argv)-1 >= 13:
- set_data.append(tuple(sys.argv[10:13]))
-pdf_file = sys.argv[-1]
-n = len(set_data)
-print "Doing %i-way Venn Diagram" % n
-
-def load_ids(filename, filetype):
- if filetype=="tabular":
- for line in open(filename):
- line = line.rstrip("\n")
- if line and not line.startswith("#"):
- yield line.split("\t",1)[0]
- elif filetype=="fasta":
- for line in open(filename):
- if line.startswith(">"):
- yield line[1:].rstrip("\n").split(None,1)[0]
- elif filetype.startswith("fastq"):
- #Use the Galaxy library not Biopython to cope with CS
- from galaxy_utils.sequence.fastq import fastqReader
- handle = open(filename, "rU")
- for record in fastqReader(handle):
- #The [1:] is because the fastaReader leaves the @ on the identifer.
- yield record.identifier.split()[0][1:]
- handle.close()
- elif filetype=="sff":
- try:
- from Bio.SeqIO import index
- except ImportError:
- stop_err("Require Biopython 1.54 or later (to read SFF files)")
- #This will read the SFF index block if present (very fast)
- for name in index(filename, "sff"):
- yield name
- else:
- stop_err("Unexpected file type %s" % filetype)
-
-def load_ids_whitelist(filename, filetype, whitelist):
- for name in load_ids(filename, filetype):
- if name in whitelist:
- yield name
- else:
- stop_err("Unexpected ID %s in %s file %s" % (name, filetype, filename))
-
-if all_file in ["", "-", '""', '"-"']:
- #Load without white list
- sets = [set(load_ids(f,t)) for (f,t,c) in set_data]
- #Take union
- all = set()
- for s in sets:
- all.update(s)
- print "Inferred total of %i IDs" % len(all)
-else:
- all = set(load_ids(all_file, all_type))
- print "Total of %i IDs" % len(all)
- sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data]
-
-for s, (f,t,c) in zip(sets, set_data):
- print "%i in %s" % (len(s), c)
-
-#Now call R library to draw simple Venn diagram
-try:
- #Create dummy Venn diagram counts object for three groups
- cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n))
- rpy.r('groups <- cbind(%s)' % ','.join(['1']*n))
- rpy.r('colnames(groups) <- %s' % cols)
- rpy.r('vc <- vennCounts(groups)')
- #Populate the 2^n classes with real counts
- #Don't make any assumptions about the class order
- #print rpy.r('vc')
- for index, row in enumerate(rpy.r('vc[,%s]' % cols)):
- if isinstance(row, int) or isinstance(row, float):
- #Hack for rpy being too clever for single element row
- row = [row]
- names = all
- for wanted, s in zip(row, sets):
- if wanted:
- names = names.intersection(s)
- else:
- names = names.difference(s)
- rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names)))
- #print rpy.r('vc')
- if n == 1:
- #Single circle, don't need to add (Total XXX) line
- names = [c for (t,f,c) in set_data]
- else:
- names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)]
- rpy.r.assign("names", names)
- rpy.r.assign("colors", ["red","green","blue"][:n])
- rpy.r.pdf(pdf_file, 8, 8)
- rpy.r("""vennDiagram(vc, include="both", names=names,
- main="%s", sub="(Total %i)",
- circle.col=colors)
- """ % (all_label, len(all)))
- rpy.r.dev_off()
-except Exception, exc:
- stop_err( "%s" %str( exc ) )
-rpy.r.quit( save="no" )
-print "Done"
diff -r 978617e4b6a4 -r b7d17d1228d9 tools/plotting/venn_list.rst
--- a/tools/plotting/venn_list.rst Tue Sep 17 12:02:42 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
-Galaxy tool to draw a Venn Diagram with up to 3 sets
-====================================================
-
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (using both the Galaxy and Biopython library
-functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
-sets, which are then drawn using the R limma package function vennDiagram
-(called from Python using rpy).
-
-There are just two files to install:
-
-* venn_list.py (the Python script)
-* venn_list.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/plotting next to other
-graph drawing tools.
-
-You will also need to install Biopython 1.54 or later, and the R/Bioconductor
-pacakge limma. You should already have rpy installed for other Galaxy tools.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
-tool. The suggested location is in the "Graph/Display Data" section. Simply add
-the line::
-
-
-
-If you wish to run the unit tests, also add this to tools_conf.xml.sample and
-move/copy the test-data files under Galaxy's test-data folder. Then::
-
- ./run_functional_tests.sh -id venn_list
-
-
-History
-=======
-
-======= ======================================================================
-Version Changes
-------- ----------------------------------------------------------------------
-v0.0.3 - Initial public release.
-v0.0.4 - Ignore blank lines when loading IDs from tabular files
-v0.0.5 - Explicit Galaxy error handling of return codes
-v0.0.6 - Added unit tests.
- - Use reStructuredText for this README file.
- - Adopt standard MIT licence.
- - Updated citation information (Cock et al. 2013).
- - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
-======= ======================================================================
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-Development has now moved to a dedicated GitHub repository:
-https://github.com/peterjc/pico_galaxy/tree/master/tools
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
-
- $ tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
-
-Check this worked::
-
- $ tar -tzf venn_list.tar.gz
- tools/plotting/venn_list.py
- tools/plotting/venn_list.rst
- tools/plotting/venn_list.xml
- test-data/venn_list1.pdf
- test-data/venn_list.tabular
- test-data/rhodopsin_proteins.fasta
-
-
-Licence (MIT)
-=============
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
diff -r 978617e4b6a4 -r b7d17d1228d9 tools/plotting/venn_list.xml
--- a/tools/plotting/venn_list.xml Tue Sep 17 12:02:42 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-
- from lists
-
- rpy
- Bio
-
-
-venn_list.py
-#if $universe.type_select=="implicit":
- - -
-#else:
- $main $main.ext
-#end if
-"$main_lab"
-#for $s in $sets:
- $s.set $s.set.ext "$s.lab"
-#end for
-$PDF
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-.. class:: infomark
-
-**TIP:** If your data is in tabular files, the identifier is assumed to be in column one.
-
-**What it does**
-
-Draws Venn Diagram for one, two or three sets (as a PDF file).
-
-You must supply one, two or three sets of identifiers -- corresponding
-to one, two or three circles on the Venn Diagram.
-
-In general you should also give the full list of all the identifiers
-explicitly. This is used to calculate the number of identifers outside
-the circles (and check the identifiers in the other files match up).
-The full list can be omitted by implicitly taking the union of the
-category sets. In this case, the count outside the categories (circles)
-will always be zero.
-
-The identifiers can be taken from the first column of a tabular file
-(e.g. query names in BLAST tabular output, or signal peptide predictions
-after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).
-
-For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF
-file), and the results of several different read mappings (e.g. to
-different references) as tabular files (filtered to have just the mapped
-reads). You could then show the different mappings (and their overlaps)
-as a Venn Diagram, and the outside count would be the unmapped reads.
-
-**Citations**
-
-The Venn Diagrams are drawn using Gordon Smyth's limma package from
-R/Bioconductor, http://www.bioconductor.org/
-
-The R library is called from Python via rpy, http://rpy.sourceforge.net/
-
-If you use this Galaxy tool in work leading to a scientific publication please
-cite:
-
-Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
-Galaxy tools and workflows for sequence analysis with applications
-in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
-
-This tool uses Biopython to read and write SFF files, so you may also wish to
-cite the Biopython application note (and Galaxy too of course):
-
-Cock et al 2009. Biopython: freely available Python tools for computational
-molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
-
-
-
diff -r 978617e4b6a4 -r b7d17d1228d9 tools/venn_list/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/README.rst Wed Apr 29 10:57:14 2015 -0400
@@ -0,0 +1,118 @@
+Galaxy tool to draw a Venn Diagram with up to 3 sets
+====================================================
+
+This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (using both the Galaxy and Biopython library
+functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
+sets, which are then drawn using the R limma package function vennDiagram
+(called from Python using rpy).
+
+This tool is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download the tool
+and the Biopython dependency.
+
+You will still need to install the R/Bioconductor package limma.
+
+
+Manual Installation
+===================
+
+There are just two files to install:
+
+* ``venn_list.py`` (the Python script)
+* ``venn_list.xml`` (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder ``tools/plotting`` next to other
+graph drawing tools, or a dedicated ``tools/venn_list`` directory.
+
+You will also need to install Biopython 1.54 or later, and the R/Bioconductor
+package limma. You should already have rpy installed for other Galaxy tools.
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
+tool. The suggested location is in the "Graph/Display Data" section. Simply add
+the line::
+
+
+
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+ ./run_tests.sh -id venn_list
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.3 - Initial public release.
+v0.0.4 - Ignore blank lines when loading IDs from tabular files
+v0.0.5 - Explicit Galaxy error handling of return codes
+v0.0.6 - Added unit tests.
+ - Use reStructuredText for this README file.
+ - Adopt standard MIT licence.
+ - Updated citation information (Cock et al. 2013).
+ - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.7 - Renamed folder and README file.
+ - Tool definition now embeds citation information.
+v0.0.8 - Reorder XML elements (internal change only).
+ - Fixed and improved error handling when rpy is not available.
+ - Test output relaxed to cope with more variation in PDF output.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+ $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
+
+Check this worked::
+
+ $ tar -tzf venn_list.tar.gz
+ tools/venn_list/README.rst
+ tools/venn_list/venn_list.py
+ tools/venn_list/venn_list.xml
+ test-data/magic.pdf
+ test-data/venn_list.tabular
+ test-data/rhodopsin_proteins.fasta
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r 978617e4b6a4 -r b7d17d1228d9 tools/venn_list/venn_list.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/venn_list.py Wed Apr 29 10:57:14 2015 -0400
@@ -0,0 +1,137 @@
+#!/usr/bin/env python
+"""Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy)
+
+This script is copyright 2010 by Peter Cock, The James Hutton Institute
+(formerly SCRI), UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.8 of the script.
+"""
+
+
+import sys
+
+def sys_exit(msg, error_level=1):
+ """Print error message to stdout and quit with given error level."""
+ sys.stderr.write("%s\n" % msg)
+ sys.exit(error_level)
+
+try:
+ import rpy
+except ImportError:
+ sys_exit("Requires the Python library rpy (to call R)")
+except RuntimeError, e:
+ sys_exit("The Python library rpy is not availble for the current R version\n\n%s" % e)
+
+try:
+ rpy.r.library("limma")
+except:
+ sys_exit("Requires the R library limma (for vennDiagram function)")
+
+
+if len(sys.argv)-1 not in [7, 10, 13]:
+ sys_exit("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1))
+
+all_file, all_type, all_label = sys.argv[1:4]
+set_data = []
+if len(sys.argv)-1 >= 7:
+ set_data.append(tuple(sys.argv[4:7]))
+if len(sys.argv)-1 >= 10:
+ set_data.append(tuple(sys.argv[7:10]))
+if len(sys.argv)-1 >= 13:
+ set_data.append(tuple(sys.argv[10:13]))
+pdf_file = sys.argv[-1]
+n = len(set_data)
+print "Doing %i-way Venn Diagram" % n
+
+def load_ids(filename, filetype):
+ if filetype=="tabular":
+ for line in open(filename):
+ line = line.rstrip("\n")
+ if line and not line.startswith("#"):
+ yield line.split("\t",1)[0]
+ elif filetype=="fasta":
+ for line in open(filename):
+ if line.startswith(">"):
+ yield line[1:].rstrip("\n").split(None,1)[0]
+ elif filetype.startswith("fastq"):
+ #Use the Galaxy library not Biopython to cope with CS
+ from galaxy_utils.sequence.fastq import fastqReader
+ handle = open(filename, "rU")
+ for record in fastqReader(handle):
+ #The [1:] is because the fastaReader leaves the @ on the identifer.
+ yield record.identifier.split()[0][1:]
+ handle.close()
+ elif filetype=="sff":
+ try:
+ from Bio.SeqIO import index
+ except ImportError:
+ sys_exit("Require Biopython 1.54 or later (to read SFF files)")
+ #This will read the SFF index block if present (very fast)
+ for name in index(filename, "sff"):
+ yield name
+ else:
+ sys_exit("Unexpected file type %s" % filetype)
+
+def load_ids_whitelist(filename, filetype, whitelist):
+ for name in load_ids(filename, filetype):
+ if name in whitelist:
+ yield name
+ else:
+ sys_exit("Unexpected ID %s in %s file %s" % (name, filetype, filename))
+
+if all_file in ["", "-", '""', '"-"']:
+ #Load without white list
+ sets = [set(load_ids(f,t)) for (f,t,c) in set_data]
+ #Take union
+ all = set()
+ for s in sets:
+ all.update(s)
+ print "Inferred total of %i IDs" % len(all)
+else:
+ all = set(load_ids(all_file, all_type))
+ print "Total of %i IDs" % len(all)
+ sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data]
+
+for s, (f,t,c) in zip(sets, set_data):
+ print "%i in %s" % (len(s), c)
+
+#Now call R library to draw simple Venn diagram
+try:
+ #Create dummy Venn diagram counts object for three groups
+ cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n))
+ rpy.r('groups <- cbind(%s)' % ','.join(['1']*n))
+ rpy.r('colnames(groups) <- %s' % cols)
+ rpy.r('vc <- vennCounts(groups)')
+ #Populate the 2^n classes with real counts
+ #Don't make any assumptions about the class order
+ #print rpy.r('vc')
+ for index, row in enumerate(rpy.r('vc[,%s]' % cols)):
+ if isinstance(row, int) or isinstance(row, float):
+ #Hack for rpy being too clever for single element row
+ row = [row]
+ names = all
+ for wanted, s in zip(row, sets):
+ if wanted:
+ names = names.intersection(s)
+ else:
+ names = names.difference(s)
+ rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names)))
+ #print rpy.r('vc')
+ if n == 1:
+ #Single circle, don't need to add (Total XXX) line
+ names = [c for (t,f,c) in set_data]
+ else:
+ names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)]
+ rpy.r.assign("names", names)
+ rpy.r.assign("colors", ["red","green","blue"][:n])
+ rpy.r.pdf(pdf_file, 8, 8)
+ rpy.r("""vennDiagram(vc, include="both", names=names,
+ main="%s", sub="(Total %i)",
+ circle.col=colors)
+ """ % (all_label, len(all)))
+ rpy.r.dev_off()
+except Exception, exc:
+ sys_exit( "%s" %str( exc ) )
+rpy.r.quit( save="no" )
+print "Done"
diff -r 978617e4b6a4 -r b7d17d1228d9 tools/venn_list/venn_list.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/venn_list.xml Wed Apr 29 10:57:14 2015 -0400
@@ -0,0 +1,130 @@
+
+ from lists
+
+ rpy
+ biopython
+ Bio
+
+
+
+
+
+
+
+venn_list.py
+#if $universe.type_select=="implicit":
+ - -
+#else:
+ "$main" $main.ext
+#end if
+"$main_lab"
+#for $s in $sets:
+ "$s.set" $s.set.ext "$s.lab"
+#end for
+$PDF
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+.. class:: infomark
+
+**TIP:** If your data is in tabular files, the identifier is assumed to be in column one.
+
+**What it does**
+
+Draws Venn Diagram for one, two or three sets (as a PDF file).
+
+You must supply one, two or three sets of identifiers -- corresponding
+to one, two or three circles on the Venn Diagram.
+
+In general you should also give the full list of all the identifiers
+explicitly. This is used to calculate the number of identifers outside
+the circles (and check the identifiers in the other files match up).
+The full list can be omitted by implicitly taking the union of the
+category sets. In this case, the count outside the categories (circles)
+will always be zero.
+
+The identifiers can be taken from the first column of a tabular file
+(e.g. query names in BLAST tabular output, or signal peptide predictions
+after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).
+
+For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF
+file), and the results of several different read mappings (e.g. to
+different references) as tabular files (filtered to have just the mapped
+reads). You could then show the different mappings (and their overlaps)
+as a Venn Diagram, and the outside count would be the unmapped reads.
+
+**Citations**
+
+The Venn Diagrams are drawn using Gordon Smyth's limma package from
+R/Bioconductor, http://www.bioconductor.org/
+
+The R library is called from Python via rpy, http://rpy.sourceforge.net/
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This tool uses Biopython to read and write SFF files, so you may also wish to
+cite the Biopython application note (and Galaxy too of course):
+
+Cock et al 2009. Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+
+
+ 10.7717/peerj.167
+ 10.1093/bioinformatics/15.5.356
+
+