# HG changeset patch
# User peterjc
# Date 1307481787 14400
# Node ID 5b552b3005f261de219f0a44c2ddc760d00fd3d0
# Parent  5cd569750e8581cb99d13888bbacfe07209bfccb
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository

diff -r 5cd569750e85 -r 5b552b3005f2 tools/fasta_tools/fasta_filter_by_id.py
--- a/tools/fasta_tools/fasta_filter_by_id.py	Tue Jun 07 17:22:48 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.py	Tue Jun 07 17:23:07 2011 -0400
@@ -12,6 +12,11 @@
 Note in the default NCBI BLAST+ tabular output, the query sequence ID is
 in column one, and the ID of the match from the database is in column two.
 Here sensible values for the column numbers would therefore be "1" or "2".
+
+This script is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.3 of the script.
 """
 import sys
 from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
diff -r 5cd569750e85 -r 5b552b3005f2 tools/fasta_tools/fasta_filter_by_id.txt
--- a/tools/fasta_tools/fasta_filter_by_id.txt	Tue Jun 07 17:22:48 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.txt	Tue Jun 07 17:23:07 2011 -0400
@@ -1,3 +1,12 @@
+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+This tool is now obsolete, having been replaced	by a more general version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 FASTA sequences by ID
 ===========================================
 
@@ -33,12 +42,16 @@
 v0.0.1 - Initial version (not publicly released)
 v0.0.2 - Allow both, just pos or just neg output files
 v0.0.3 - Include FASTA in tool name
+v0.0.4 - Deprecated, marked as hidden in the XML
+
 
 Developers
 ==========
 
-This script and similar versions for FASTQ and SFF files are currently being
-developed on the following hg branch:
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+This incorporates the previously used hg branch:
 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
 
 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
diff -r 5cd569750e85 -r 5b552b3005f2 tools/fasta_tools/fasta_filter_by_id.xml
--- a/tools/fasta_tools/fasta_filter_by_id.xml	Tue Jun 07 17:22:48 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.xml	Tue Jun 07 17:23:07 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.3">
+<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.4" hidden="true">
 	<description>from a tabular file</description>
 	<command interpreter="python">
 fasta_filter_by_id.py $input_tabular $columns $input_fasta
@@ -64,6 +64,12 @@
 	</tests>
 	<help>
 
+**Deprecated**
+
+This tool is now obsolete, and should not be used in future. It has been
+replaced by a more general version covering FASTA, FASTQ and SFF in one
+single tool.
+
 **What it does**
 
 By default it divides a FASTA file in two, those sequences with or without an