# HG changeset patch
# User peterjc
# Date 1431442176 14400
# Node ID 493c0fa29239015cf573ae63a3ad6b541e7ad7ff
# Parent  367a0403b7d2868f5e8b7ac00943021513939abd
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit c79c4d1dfaabaea4d7da9ec1c808c41c4b0d451f

diff -r 367a0403b7d2 -r 493c0fa29239 README.rst
--- a/README.rst	Thu May 07 05:43:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-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::
-
-  <tool file="venn_list/venn_list.xml" />
-
-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.
-        - Declare Biopython dependency via the Tool Shed.
-======= ======================================================================
-
-
-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 pushing a release to the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/
-use the following Planemo command (which requires you have set your Tool Shed
-access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
-
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list/
-    ...
-    $ tar -tzf shed_upload.tar.gz 
-    README.rst
-    test-data/magic.pdf
-    test-data/rhodopsin_proteins.fasta
-    test-data/venn_list.tabular
-    tool_dependencies.xml
-    venn_list.py
-    venn_list.xml
-
-This tar-ball can be uploaded to the Tool Shed via the web interface (using
-the ``--tar`` command or via
-Planemo. More simply, the following single command can be used:
-
-    $ planemo shed_upload 
-
-
-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 367a0403b7d2 -r 493c0fa29239 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 07 05:43:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.65">
-        <repository changeset_revision="f8d72690eeae" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r 367a0403b7d2 -r 493c0fa29239 tools/venn_list/README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/README.rst	Tue May 12 10:49:36 2015 -0400
@@ -0,0 +1,124 @@
+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::
+
+  <tool file="venn_list/venn_list.xml" />
+
+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.
+        - Declare Biopython dependency via the Tool Shed.
+======= ======================================================================
+
+
+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 pushing a release to the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/
+use the following Planemo command (which requires you have set your Tool Shed
+access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    tools/venn_list/README.rst
+    tools/venn_list/tool_dependencies.xml
+    tools/venn_list/venn_list.py
+    tools/venn_list/venn_list.xml
+    test-data/magic.pdf
+    test-data/rhodopsin_proteins.fasta
+    test-data/venn_list.tabular
+
+
+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 367a0403b7d2 -r 493c0fa29239 tools/venn_list/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/tool_dependencies.xml	Tue May 12 10:49:36 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="biopython" version="1.65">
+        <repository changeset_revision="f8d72690eeae" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
diff -r 367a0403b7d2 -r 493c0fa29239 tools/venn_list/venn_list.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/venn_list.py	Tue May 12 10:49:36 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 367a0403b7d2 -r 493c0fa29239 tools/venn_list/venn_list.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/venn_list/venn_list.xml	Tue May 12 10:49:36 2015 -0400
@@ -0,0 +1,130 @@
+<tool id="venn_list" name="Venn Diagram" version="0.0.8">
+    <description>from lists</description>
+    <requirements>
+        <requirement type="python-module">rpy</requirement>
+        <requirement type="package" version="1.65">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <command interpreter="python">
+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
+    </command>
+    <inputs>
+        <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
+        <conditional name="universe">
+            <param name="type_select" type="select" label="Implicit or explicit full ID list?">
+                <option value="explicit">Explicit</option>
+                <option value="implicit">Implicit (use union of sets below)</option>
+            </param>
+            <when value="explicit">
+                 <param name="main" type="data" format="tabular,fasta,fastq,sff" label="Full dataset (with all identifiers)" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>
+            </when>
+            <when value="implicit"/>
+        </conditional>
+        <repeat name="sets" min="1" max="3" title="Sets">
+            <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>
+            <param name="lab" size="30" type="text" value="Group" label="Caption for set"/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="PDF" />
+    </outputs>
+    <tests>
+         <!-- Doesn't seem to work properly, manages to get two sets, both
+              with same FASTA file, but second with default "Group" label. -->
+        <test>
+            <param name="type_select" value="explicit"/>
+            <param name="main" value="venn_list.tabular" ftype="tabular"/>
+            <param name="main_lab" value="Some Proteins"/>
+            <param name="set" value="rhodopsin_proteins.fasta"/>
+            <param name="lab" value="Rhodopsins"/>
+            <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
+        </test>
+        <!-- Can't use more than one repeat value in tests (yet)
+        <test>
+            <param name="type_select" value="explicit"/>
+            <param name="main" value="venn_list.tabular" ftype="tabular"/>
+            <param name="main_lab" value="Some Proteins"/>
+            <param name="count" value="3"/>
+            <param name="set" value="rhodopsin_proteins.fasta"/>
+            <param name="lab" value="Rhodopsins"/>
+            <param name="set" value="four_human_proteins.fasta"/>
+            <param name="lab" value="Human"/>
+            <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/>
+            <param name="lab" value="Human vs Rhodopsin BLAST"/>
+            <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
+        </test>
+        -->
+    </tests>
+    <help>
+
+.. 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.
+
+    </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/15.5.356</citation>
+    </citations>
+</tool>
diff -r 367a0403b7d2 -r 493c0fa29239 venn_list.py
--- a/venn_list.py	Thu May 07 05:43:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,137 +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 0.0.8 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 367a0403b7d2 -r 493c0fa29239 venn_list.xml
--- a/venn_list.xml	Thu May 07 05:43:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-<tool id="venn_list" name="Venn Diagram" version="0.0.8">
-    <description>from lists</description>
-    <requirements>
-        <requirement type="python-module">rpy</requirement>
-        <requirement type="package" version="1.65">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
-    </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <command interpreter="python">
-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
-    </command>
-    <inputs>
-        <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
-        <conditional name="universe">
-            <param name="type_select" type="select" label="Implicit or explicit full ID list?">
-                <option value="explicit">Explicit</option>
-                <option value="implicit">Implicit (use union of sets below)</option>
-            </param>
-            <when value="explicit">
-                 <param name="main" type="data" format="tabular,fasta,fastq,sff" label="Full dataset (with all identifiers)" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>
-            </when>
-            <when value="implicit"/>
-        </conditional>
-        <repeat name="sets" min="1" max="3" title="Sets">
-            <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>
-            <param name="lab" size="30" type="text" value="Group" label="Caption for set"/>
-        </repeat>
-    </inputs>
-    <outputs>
-        <data format="pdf" name="PDF" />
-    </outputs>
-    <tests>
-         <!-- Doesn't seem to work properly, manages to get two sets, both
-              with same FASTA file, but second with default "Group" label. -->
-        <test>
-            <param name="type_select" value="explicit"/>
-            <param name="main" value="venn_list.tabular" ftype="tabular"/>
-            <param name="main_lab" value="Some Proteins"/>
-            <param name="set" value="rhodopsin_proteins.fasta"/>
-            <param name="lab" value="Rhodopsins"/>
-            <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
-        </test>
-        <!-- Can't use more than one repeat value in tests (yet)
-        <test>
-            <param name="type_select" value="explicit"/>
-            <param name="main" value="venn_list.tabular" ftype="tabular"/>
-            <param name="main_lab" value="Some Proteins"/>
-            <param name="count" value="3"/>
-            <param name="set" value="rhodopsin_proteins.fasta"/>
-            <param name="lab" value="Rhodopsins"/>
-            <param name="set" value="four_human_proteins.fasta"/>
-            <param name="lab" value="Human"/>
-            <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/>
-            <param name="lab" value="Human vs Rhodopsin BLAST"/>
-            <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
-        </test>
-        -->
-    </tests>
-    <help>
-
-.. 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.
-
-    </help>
-    <citations>
-        <citation type="doi">10.7717/peerj.167</citation>
-        <citation type="doi">10.1093/bioinformatics/15.5.356</citation>
-    </citations>
-</tool>