# HG changeset patch
# User peterjc
# Date 1382952105 14400
# Node ID 6842c0c7bc70b6d2421515fe4f16a4008d82aea0
# Parent  19e26966ed3e7805592801e08d6495855609fac0
Uploaded v0.0.7, depend on Biopython 1.62, tabs to spaces in XML

diff -r 19e26966ed3e -r 6842c0c7bc70 tools/filters/repository_dependencies.xml
--- a/tools/filters/repository_dependencies.xml	Mon Jul 29 09:13:13 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="This requires Biopython as a dependency.">
-<!-- Leave out the tool shed and revision to get the current
-     tool shed and latest revision at the time of upload -->
-<repository changeset_revision="5d0c54f7fea2" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
-</repositories>
diff -r 19e26966ed3e -r 6842c0c7bc70 tools/filters/seq_select_by_id.py
--- a/tools/filters/seq_select_by_id.py	Mon Jul 29 09:13:13 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-#!/usr/bin/env python
-"""Select FASTA, QUAL, FASTQ or SSF sequences by IDs from a tabular file.
-
-Takes five command line options, tabular filename, ID column number (using
-one based counting), input filename, input type (e.g. FASTA or SFF) and the
-output filename (same format as input sequence file).
-
-When selecting from an SFF file, any Roche XML manifest in the input file is
-preserved in both output files.
-
-This tool is a short Python script which requires Biopython 1.54 or later
-for SFF file support. If you use this tool in scientific work leading to a
-publication, please cite the Biopython application note:
-
-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.
-
-This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK.
-All rights reserved. See accompanying text file for licence details (MIT
-license).
-
-This is version 0.0.6 of the script.
-"""
-import sys
-
-def stop_err(msg, err=1):
-    sys.stderr.write(msg.rstrip() + "\n")
-    sys.exit(err)
-
-if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.6"
-    sys.exit(0)
-
-#Parse Command Line
-try:
-    tabular_file, col_arg, in_file, seq_format, out_file = sys.argv[1:]
-except ValueError:
-    stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
-try:
-    if col_arg.startswith("c"):
-        column = int(col_arg[1:])-1
-    else:
-        column = int(col_arg)-1
-except ValueError:
-    stop_err("Expected column number, got %s" % col_arg)
-
-if seq_format == "fastqcssanger":
-    stop_err("Colorspace FASTQ not supported.")
-elif seq_format.lower() in ["sff", "fastq", "qual", "fasta"]:
-    seq_format = seq_format.lower()
-elif seq_format.lower().startswith("fastq"):
-    #We don't care how the qualities are encoded    
-    seq_format = "fastq"
-elif seq_format.lower().startswith("qual"):
-    #We don't care what the scores are
-    seq_format = "qual"
-else:
-    stop_err("Unrecognised file format %r" % seq_format)
-
-
-try:
-    from Bio import SeqIO
-except ImportError:
-    stop_err("Biopython 1.54 or later is required")
-
-
-def parse_ids(tabular_file, col):
-    """Read tabular file and record all specified identifiers."""
-    handle = open(tabular_file, "rU")
-    for line in handle:
-        if line.strip() and not line.startswith("#"):
-            yield line.rstrip("\n").split("\t")[col].strip()
-    handle.close()
-
-#Index the sequence file.
-#If very big, could use SeqIO.index_db() to avoid memory bottleneck...
-records = SeqIO.index(in_file, seq_format)
-print "Indexed %i sequences" % len(records)
-
-if seq_format.lower()=="sff":
-    #Special case to try to preserve the XML manifest
-    try:
-        from Bio.SeqIO.SffIO import SffIterator, SffWriter
-    except ImportError:
-        stop_err("Requires Biopython 1.54 or later")
-
-    try:
-        from Bio.SeqIO.SffIO import ReadRocheXmlManifest
-    except ImportError:
-        #Prior to Biopython 1.56 this was a private function
-        from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
-
-    in_handle = open(in_file, "rb") #must be binary mode!
-    try:
-        manifest = ReadRocheXmlManifest(in_handle)
-    except ValueError:
-        manifest = None
-    in_handle.close()
-
-    out_handle = open(out_file, "wb")
-    writer = SffWriter(out_handle, xml=manifest)
-    count = 0
-    #This does have the overhead of parsing into SeqRecord objects,
-    #but doing the header and index at the low level is too fidly.
-    iterator = (records[name] for name in parse_ids(tabular_file, column))
-    try:
-        count = writer.write_file(iterator)
-    except KeyError, err:
-        out_handle.close()
-        if name not in records:
-            stop_err("Identifier %r not found in sequence file" % name)
-        else:
-            raise err
-    out_handle.close()
-else:
-    #Avoid overhead of parsing into SeqRecord objects,
-    #just re-use the original formatting from the input file.
-    out_handle = open(out_file, "w")
-    count = 0
-    for name in parse_ids(tabular_file, column):
-        try:
-            out_handle.write(records.get_raw(name))
-        except KeyError:
-            out_handle.close()
-            stop_err("Identifier %r not found in sequence file" % name)
-        count += 1
-    out_handle.close()
-
-print "Selected %i sequences by ID" % count
diff -r 19e26966ed3e -r 6842c0c7bc70 tools/filters/seq_select_by_id.rst
--- a/tools/filters/seq_select_by_id.rst	Mon Jul 29 09:13:13 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
-===============================================================
-
-This tool is copyright 2011-2013 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 Biopython library functions) to extract
-sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
-by a column of a tabular file. The output order follows that of the tabular file,
-and if there are duplicates in the tabular file, there will be duplicates in the
-output sequence file.
-
-This tool is available from the Galaxy Tool Shed at:
-
-* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
-
-See also the sister tools to filter sequence files according to IDs from column(s)
-of a tabular file (where the output order follows the sequence file, and any
-duplicate IDs are ignored) and rename sequences:
-
-* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
-* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
-
-
-Automated Installation
-======================
-
-This should be straightforward using the Galaxy Tool Shed, which should be
-able to automatically install the dependency on Biopython, and then install
-this tool and run its unit tests.
-
-
-Manual Installation
-===================
-
-There are just two files to install to use this tool from within Galaxy:
-
-* seq_select_by_id.py (the Python script)
-* seq_select_by_id.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/filters next to the tool
-for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
-tool. One suggested location is in the filters section. Simply add the line::
-
-    <tool file="filters/seq_select_by_id.xml" />
-
-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 seq_select_by_id
-
-You will also need to install Biopython 1.54 or later. That's it.
-
-
-History
-=======
-
-======= ======================================================================
-Version Changes
-------- ----------------------------------------------------------------------
-v0.0.1   - Initial version.
-v0.0.3   - Ignore blank lines in input.
-v0.0.4   - Record script version when run from Galaxy.
-         - Basic unit test included.
-v0.0.5   - Check for errors using Python script's return code.
-v0.0.6   - Link to Tool Shed added to help text and this documentation.
-         - Automatic installation of Biopython dependency.
-         - Use reStructuredText for this README file.
-         - Adopt standard MIT License.
-======= ======================================================================
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/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 seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* tools/filters/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
-
-Check this worked::
-
-    $ tar -tzf seq_select_by_id.tar.gz
-    tools/filters/seq_select_by_id.py
-    tools/filters/seq_select_by_id.rst
-    tools/filter/seq_select_by_id.xml
-    tools/filters/repository_dependencies.xml
-    test-data/k12_ten_proteins.fasta
-    test-data/k12_hypothetical.fasta
-    test-data/k12_hypothetical.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 19e26966ed3e -r 6842c0c7bc70 tools/filters/seq_select_by_id.xml
--- a/tools/filters/seq_select_by_id.xml	Mon Jul 29 09:13:13 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
-	<description>from a tabular file</description>
-	<version_command interpreter="python">seq_select_by_id.py --version</version_command>
-	<command interpreter="python">
-seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
-	</command>
-        <stdio>
-                <!-- Anything other than zero is an error -->
-                <exit_code range="1:" />
-                <exit_code range=":-1" />
-        </stdio>
-	<inputs>
-		<param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
-		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
-		<param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
-	</inputs>
-	<outputs>
-		<data name="output_file" format="fasta" label="Selected sequences">
-			<!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-			<change_format>
-				<when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-				<when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-				<when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-				<when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-				<when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-				<when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-			</change_format>
-		</data>
-	</outputs>
-	<tests>
-		<test>
-			<param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" />
-			<param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
-			<param name="column" value="1" />
-			<output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" />
-		</test>
-	</tests>
-	<requirements>
-		<requirement type="python-module">Bio</requirement>
-	</requirements>
-	<help>
-
-**What it does**
-
-Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
-new sequence file (of the same format) containing only the records with identifiers
-in the tabular file (in the order from the tabular file).
-
-WARNING: If you have any duplicates in the tabular file identifiers, you will get
-duplicate sequences in the output.
-
-**Citation**
-
-This tool uses Biopython to read, write and index sequence files. If you use
-this tool in scientific work leading to a publication, please 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.
-
-This tool is available to install into other Galaxy Instances via the Galaxy
-Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
-	</help>
-</tool>
diff -r 19e26966ed3e -r 6842c0c7bc70 tools/seq_select_by_id/README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_select_by_id/README.rst	Mon Oct 28 05:21:45 2013 -0400
@@ -0,0 +1,124 @@
+Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
+===============================================================
+
+This tool is copyright 2011-2013 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 Biopython library functions) to extract
+sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
+by a column of a tabular file. The output order follows that of the tabular file,
+and if there are duplicates in the tabular file, there will be duplicates in the
+output sequence file.
+
+This tool is available from the Galaxy Tool Shed at:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
+
+See also the sister tools to filter sequence files according to IDs from column(s)
+of a tabular file (where the output order follows the sequence file, and any
+duplicate IDs are ignored) and rename sequences:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
+
+
+Automated Installation
+======================
+
+This should be straightforward using the Galaxy Tool Shed, which should be
+able to automatically install the dependency on Biopython, and then install
+this tool and run its unit tests.
+
+
+Manual Installation
+===================
+
+There are just two files to install to use this tool from within Galaxy:
+
+* seq_select_by_id.py (the Python script)
+* seq_select_by_id.xml (the Galaxy tool definition)
+
+The suggested location is a dedicated tools/seq_select_by_id folder.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. One suggested location is in the filters section. Simply add the line::
+
+    <tool file="seq_select_by_id/seq_select_by_id.xml" />
+
+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 seq_select_by_id
+
+You will also need to install Biopython 1.54 or later. That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version.
+v0.0.3  - Ignore blank lines in input.
+v0.0.4  - Record script version when run from Galaxy.
+        - Basic unit test included.
+v0.0.5  - Check for errors using Python script's return code.
+v0.0.6  - Link to Tool Shed added to help text and this documentation.
+        - Automatic installation of Biopython dependency.
+        - Use reStructuredText for this README file.
+        - Adopt standard MIT License.
+v0.0.7  - Updated citation information (Cock et al. 2013).
+        - Fixed Biopython dependency setup.
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+        - Renamed folder and adopted README.rst naming.
+======= ======================================================================
+
+
+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/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 seq_select_by_id.tar.gz tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.* tools/seq_select_by_id/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
+
+Check this worked::
+
+    $ tar -tzf seq_select_by_id.tar.gz
+    tools/seq_select_by_id/README.rst
+    tools/seq_select_by_id/seq_select_by_id.py
+    tools/seq_select_by_id/seq_select_by_id.xml
+    tools/seq_select_by_id/repository_dependencies.xml
+    test-data/k12_ten_proteins.fasta
+    test-data/k12_hypothetical.fasta
+    test-data/k12_hypothetical.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 19e26966ed3e -r 6842c0c7bc70 tools/seq_select_by_id/repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_select_by_id/repository_dependencies.xml	Mon Oct 28 05:21:45 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<repositories description="This requires Biopython as a dependency.">
+<!-- Leave out the tool shed and revision to get the current
+     tool shed and latest revision at the time of upload -->
+<repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>
diff -r 19e26966ed3e -r 6842c0c7bc70 tools/seq_select_by_id/seq_select_by_id.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_select_by_id/seq_select_by_id.py	Mon Oct 28 05:21:45 2013 -0400
@@ -0,0 +1,130 @@
+#!/usr/bin/env python
+"""Select FASTA, QUAL, FASTQ or SSF sequences by IDs from a tabular file.
+
+Takes five command line options, tabular filename, ID column number (using
+one based counting), input filename, input type (e.g. FASTA or SFF) and the
+output filename (same format as input sequence file).
+
+When selecting from an SFF file, any Roche XML manifest in the input file is
+preserved in both output files.
+
+This tool is a short Python script which requires Biopython 1.54 or later
+for SFF file support. If you use this tool in scientific work leading to a
+publication, please cite the Biopython application note:
+
+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.
+
+This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK.
+All rights reserved. See accompanying text file for licence details (MIT
+license).
+
+This is version 0.0.6 of the script.
+"""
+import sys
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg.rstrip() + "\n")
+    sys.exit(err)
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    print "v0.0.6"
+    sys.exit(0)
+
+#Parse Command Line
+try:
+    tabular_file, col_arg, in_file, seq_format, out_file = sys.argv[1:]
+except ValueError:
+    stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
+try:
+    if col_arg.startswith("c"):
+        column = int(col_arg[1:])-1
+    else:
+        column = int(col_arg)-1
+except ValueError:
+    stop_err("Expected column number, got %s" % col_arg)
+
+if seq_format == "fastqcssanger":
+    stop_err("Colorspace FASTQ not supported.")
+elif seq_format.lower() in ["sff", "fastq", "qual", "fasta"]:
+    seq_format = seq_format.lower()
+elif seq_format.lower().startswith("fastq"):
+    #We don't care how the qualities are encoded    
+    seq_format = "fastq"
+elif seq_format.lower().startswith("qual"):
+    #We don't care what the scores are
+    seq_format = "qual"
+else:
+    stop_err("Unrecognised file format %r" % seq_format)
+
+
+try:
+    from Bio import SeqIO
+except ImportError:
+    stop_err("Biopython 1.54 or later is required")
+
+
+def parse_ids(tabular_file, col):
+    """Read tabular file and record all specified identifiers."""
+    handle = open(tabular_file, "rU")
+    for line in handle:
+        if line.strip() and not line.startswith("#"):
+            yield line.rstrip("\n").split("\t")[col].strip()
+    handle.close()
+
+#Index the sequence file.
+#If very big, could use SeqIO.index_db() to avoid memory bottleneck...
+records = SeqIO.index(in_file, seq_format)
+print "Indexed %i sequences" % len(records)
+
+if seq_format.lower()=="sff":
+    #Special case to try to preserve the XML manifest
+    try:
+        from Bio.SeqIO.SffIO import SffIterator, SffWriter
+    except ImportError:
+        stop_err("Requires Biopython 1.54 or later")
+
+    try:
+        from Bio.SeqIO.SffIO import ReadRocheXmlManifest
+    except ImportError:
+        #Prior to Biopython 1.56 this was a private function
+        from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
+
+    in_handle = open(in_file, "rb") #must be binary mode!
+    try:
+        manifest = ReadRocheXmlManifest(in_handle)
+    except ValueError:
+        manifest = None
+    in_handle.close()
+
+    out_handle = open(out_file, "wb")
+    writer = SffWriter(out_handle, xml=manifest)
+    count = 0
+    #This does have the overhead of parsing into SeqRecord objects,
+    #but doing the header and index at the low level is too fidly.
+    iterator = (records[name] for name in parse_ids(tabular_file, column))
+    try:
+        count = writer.write_file(iterator)
+    except KeyError, err:
+        out_handle.close()
+        if name not in records:
+            stop_err("Identifier %r not found in sequence file" % name)
+        else:
+            raise err
+    out_handle.close()
+else:
+    #Avoid overhead of parsing into SeqRecord objects,
+    #just re-use the original formatting from the input file.
+    out_handle = open(out_file, "w")
+    count = 0
+    for name in parse_ids(tabular_file, column):
+        try:
+            out_handle.write(records.get_raw(name))
+        except KeyError:
+            out_handle.close()
+            stop_err("Identifier %r not found in sequence file" % name)
+        count += 1
+    out_handle.close()
+
+print "Selected %i sequences by ID" % count
diff -r 19e26966ed3e -r 6842c0c7bc70 tools/seq_select_by_id/seq_select_by_id.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Mon Oct 28 05:21:45 2013 -0400
@@ -0,0 +1,72 @@
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
+    <description>from a tabular file</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <version_command interpreter="python">seq_select_by_id.py --version</version_command>
+    <command interpreter="python">
+seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
+        <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
+        <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="fasta" label="Selected sequences">
+            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+            <change_format>
+                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" />
+            <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
+            <param name="column" value="1" />
+            <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
+new sequence file (of the same format) containing only the records with identifiers
+in the tabular file (in the order from the tabular file).
+
+WARNING: If you have any duplicates in the tabular file identifiers, you will get
+duplicate sequences in the output.
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+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, write and index sequence 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.
+
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
+    </help>
+</tool>