--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq_filter_by_id/README.rst	Fri Feb 03 05:34:18 2017 -0500
@@ -0,0 +1,114 @@
+Obsolete
+========
+
+This tool is now obsolete, having been replaced	by a more general version
+covering the FASTA, FASTQ and SFF sequence formats in a single tool. You
+should only install this tool if you need to support existing workflows
+which used it.
+
+Galaxy tool to filter FASTQ sequences by ID
+===========================================
+
+This tool is copyright 2010-2017 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This tool is a short Python script (using the Galaxy library functions) which
+divides a FASTQ file in two, those sequences with or without an ID present in
+the specified column(s) of a tabular file. Example uses include filtering based
+on search results from a tool like NCBI BLAST before assembly.
+
+There are just two files to install:
+
+* fastq_filter_by_id.py (the Python script)
+* fastq_filter_by_id.xml (the Galaxy tool definition)
+
+The suggested location is next to the similarly named fastq_filter.py and
+fastq_filter.xml files which are included with Galaxy, i.e. in the Galaxy
+folder tools/fastq
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer
+the tool. The suggested location is next to the fastq_filter.xml entry. Simply
+add the line:
+
+<tool file="fastq/fastq_filter_by_id.xml" />
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial verion (not publicly released)
+v0.0.2  - Allow both, just pos or just neg output files
+        - Preserve the FASTQ variant in the XML wrapper
+v0.0.3  - Fixed bug when generating non-matching FASTQ file only
+v0.0.4  - Deprecated, marked as hidden in the XML
+v0.0.5  - Explicit dependency on ``galaxy_sequence_utils``.
+        - Citation information (Cock et al. 2013).
+        - Explicitly record version via ``<version_command>``.
+        - Use ``format_source``/``metadata_source`` idiom for output format.
+        - Use standard MIT license (was previously using the MIT/BSD style
+          Biopython Licence Agreement).
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and other tools for filtering FASTA, FASTQ and SFF files were
+initially developed on the following hg branches:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+
+It is now under GitHub https://github.com/peterjc/pico_galaxy/
+
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (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_update -t testtoolshed --check_diff tools/fastq_filter_by_id/
+    ...
+
+or::
+
+    $ planemo shed_update -t toolshed --check_diff tools/fastq_filter_by_id/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only tools/fastq_filter_by_id/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    tools/fastq_filter_by_id/README.rst
+    tools/fastq_filter_by_id/fastq_filter_by_id.py
+    tools/fastq_filter_by_id/fastq_filter_by_id.xml
+    tools/fastq_filter_by_id/tool_dependencies.xml
+    test-data/empty_file.dat
+    test-data/sanger-pairs-mixed.fastq
+    test-data/sanger-pairs-names.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.