# HG changeset patch
# User peterjc
# Date 1307481768 14400
# Node ID 5cd569750e8581cb99d13888bbacfe07209bfccb
# Parent  2e5f8ad1a096972bef55a06f5cd9c55992a1989d
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository

diff -r 2e5f8ad1a096 -r 5cd569750e85 tools/fasta_tools/fasta_filter_by_id.py
--- a/tools/fasta_tools/fasta_filter_by_id.py	Tue Jun 07 17:22:24 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.py	Tue Jun 07 17:22:48 2011 -0400
@@ -3,8 +3,9 @@
 
 Takes five command line options, tabular filename, ID column numbers
 (comma separated list using one based counting), input FASTA filename, and
-two output FASTA filenames (for records with and without any BLAST hits).
-If the either output filename is just a minus sign, that file is not created.
+two output FASTA filenames (for records with and without the given IDs).
+
+If either output filename is just a minus sign, that file is not created.
 This is intended to allow output for just the matched (or just the non-matched)
 records.
 
@@ -51,7 +52,7 @@
     print "Using %i IDs from tabular file" % (len(ids))
 handle.close()
 
-#Write filtered FASTA file based on IDs from BLAST file
+#Write filtered FASTA file based on IDs from tabular file
 reader = fastaReader(open(in_file, "rU"))
 if out_positive_file != "-" and out_negative_file != "-":
     print "Generating two FASTA files"
diff -r 2e5f8ad1a096 -r 5cd569750e85 tools/fasta_tools/fasta_filter_by_id.txt
--- a/tools/fasta_tools/fasta_filter_by_id.txt	Tue Jun 07 17:22:24 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.txt	Tue Jun 07 17:22:48 2011 -0400
@@ -14,7 +14,7 @@
 * fasta_filter_by_id.py (the Python script)
 * fasta_filter_by_id.xml (the Galaxy tool definition)
 
-The suggested location is next to the similarly names fasta_filter_by_length.py
+The suggested location is next to the similarly named fasta_filter_by_length.py
 and fasta_filter_by_length.xml files which are included with Galaxy, i.e.
 in the Galaxy folder tools/fasta_tools
 
@@ -30,13 +30,15 @@
 History
 =======
 
-v0.0.1 - Initial verion (not publicly released)
+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
 
 Developers
 ==========
 
-These wrappers are currently being developed on the following hg branch:
+This script and similar versions for FASTQ and SFF files are currently being
+developed on the following 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 2e5f8ad1a096 -r 5cd569750e85 tools/fasta_tools/fasta_filter_by_id.xml
--- a/tools/fasta_tools/fasta_filter_by_id.xml	Tue Jun 07 17:22:24 2011 -0400
+++ b/tools/fasta_tools/fasta_filter_by_id.xml	Tue Jun 07 17:22:48 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="fasta_filter_by_id" name="Filter sequences by ID" version="0.0.2">
+<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.3">
 	<description>from a tabular file</description>
 	<command interpreter="python">
 fasta_filter_by_id.py $input_tabular $columns $input_fasta
@@ -73,5 +73,12 @@
 Note that the order of sequences in the original FASTA file is preserved.
 Also, if any sequences share an identifier, duplicates are not removed.
 
+**Example Usage**
+
+Given a FASTA file of proteins you might run a signal peptide search (e.g.
+via the SignalP wrapper for Galaxy), then filtered these tabular results to
+select just those with a signal peptide. You could then use this tool to get
+a FASTA file of only the proteins with predicted signal peptides.
+
 	</help>
 </tool>