changeset 1:9cd3591f6afa default tip

Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository

--- a/tools/filters/sff_filter_by_id.py	Tue Jun 07 17:24:49 2011 -0400
+++ b/tools/filters/sff_filter_by_id.py	Tue Jun 07 17:25:08 2011 -0400
@@ -5,11 +5,28 @@
 (comma separated list using one based counting), input SFF filename, and
 two output SFF 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.
+
 Any Roche XML manifest in the input file is preserved in both output files.
 
 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 tool is a short Python script which requires Biopython 1.54 or later.
+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 2010 by Peter Cock, SCRI, UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.1 of the script.
 """
 import sys
 

--- a/tools/filters/sff_filter_by_id.txt	Tue Jun 07 17:24:49 2011 -0400
+++ b/tools/filters/sff_filter_by_id.txt	Tue Jun 07 17:25:08 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+This tool is now obsolete, having been replaced by a more general version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 SFF sequences by ID
 =========================================
 
@@ -30,13 +39,16 @@
 =======
 
 v0.0.1 - Initial version
+v0.0.2 - Deprecated, marked as hidden in the XML.
 
 
 Developers
 ==========
 
-This script and similar versions for FASTA and FASTQ 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

--- a/tools/filters/sff_filter_by_id.xml	Tue Jun 07 17:24:49 2011 -0400
+++ b/tools/filters/sff_filter_by_id.xml	Tue Jun 07 17:25:08 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="sff_filter_by_id" name="Filter SFF by ID" version="0.0.1">
+<tool id="sff_filter_by_id" name="Filter SFF by ID" version="0.0.2" hidden="true">
 	<description>from a tabular file</description>
 	<command interpreter="python">
 sff_filter_by_id.py $input_tabular $columns $input_sff
@@ -43,6 +43,12 @@
 	</requirements>
 	<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 Standard Flowgram Format (SFF) file in two, those
@@ -62,7 +68,7 @@
 reads without BLAST matches (i.e. those which do not match your contaminant
 database).
 
-** Citation **
+**Citation**
 
 This tool uses Biopython to read and write SFF files. If you use this tool in
 scientific work leading to a publication, please cite the Biopython application