| Previous changeset 1:d85a0608e849 (2011-06-07) Next changeset 3:d05fadb1c7b5 (2013-04-12) |
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Commit message:
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository |
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modified:
tools/fasta_tools/fasta_filter_by_id.py tools/fasta_tools/fasta_filter_by_id.txt tools/fasta_tools/fasta_filter_by_id.xml |
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| diff -r d85a0608e849 -r d1a2d254fba2 tools/fasta_tools/fasta_filter_by_id.py --- a/tools/fasta_tools/fasta_filter_by_id.py Tue Jun 07 16:33:48 2011 -0400 +++ b/tools/fasta_tools/fasta_filter_by_id.py Tue Jun 07 16:34:21 2011 -0400 |
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| @@ -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 |
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| diff -r d85a0608e849 -r d1a2d254fba2 tools/fasta_tools/fasta_filter_by_id.txt --- a/tools/fasta_tools/fasta_filter_by_id.txt Tue Jun 07 16:33:48 2011 -0400 +++ b/tools/fasta_tools/fasta_filter_by_id.txt Tue Jun 07 16:34:21 2011 -0400 |
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| @@ -1,3 +1,12 @@ +Obsolete +======== + +This tool is now obsolete, having been replaced by a more general version +covering the FASTA, FASTQ and SFF sequence formats in a single tool.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 |
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| diff -r d85a0608e849 -r d1a2d254fba2 tools/fasta_tools/fasta_filter_by_id.xml --- a/tools/fasta_tools/fasta_filter_by_id.xml Tue Jun 07 16:33:48 2011 -0400 +++ b/tools/fasta_tools/fasta_filter_by_id.xml Tue Jun 07 16:34:21 2011 -0400 |
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| @@ -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 |