Mercurial > repos > peterjc > seq_filter_by_id
changeset 8:2d4537dbf0bc draft
v0.2.6 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
| author | peterjc |
|---|---|
| date | Wed, 10 May 2017 13:18:01 -0400 |
| parents | fb1313d79396 |
| children | 141612f8c3e3 |
| files | tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.py tools/seq_filter_by_id/seq_filter_by_id.xml tools/seq_filter_by_id/tool_dependencies.xml |
| diffstat | 4 files changed, 10 insertions(+), 6 deletions(-) [+] |
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--- a/tools/seq_filter_by_id/README.rst Fri Nov 04 08:11:08 2016 -0400 +++ b/tools/seq_filter_by_id/README.rst Wed May 10 13:18:01 2017 -0400 @@ -1,7 +1,7 @@ Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID ========================================================= -This tool is copyright 2010-2015 by Peter Cock, The James Hutton Institute +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. @@ -91,6 +91,7 @@ (internal change only). v0.2.4 - Corrected error message wording. v0.2.5 - Ignore empty names, common in R output (Gildas Le Corguillé). +v0.2.6 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. ======= ======================================================================
--- a/tools/seq_filter_by_id/seq_filter_by_id.py Fri Nov 04 08:11:08 2016 -0400 +++ b/tools/seq_filter_by_id/seq_filter_by_id.py Wed May 10 13:18:01 2017 -0400 @@ -27,9 +27,11 @@ Use -v or --version to get the version, -h or --help for help. """ + import os +import re import sys -import re + from optparse import OptionParser # Parse Command Line @@ -144,6 +146,7 @@ "using first word only. e.g.:\n%s\n" % name return parts[0] + if drop_suffices: def clean_name(name): """Remove suffix."""
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml Fri Nov 04 08:11:08 2016 -0400 +++ b/tools/seq_filter_by_id/seq_filter_by_id.xml Wed May 10 13:18:01 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.5"> +<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.6"> <description>from a tabular file</description> <requirements> - <requirement type="package" version="1.64">biopython</requirement> + <requirement type="package" version="1.67">biopython</requirement> </requirements> <stdio> <!-- Anything other than zero is an error -->
--- a/tools/seq_filter_by_id/tool_dependencies.xml Fri Nov 04 08:11:08 2016 -0400 +++ b/tools/seq_filter_by_id/tool_dependencies.xml Wed May 10 13:18:01 2017 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.64"> - <repository changeset_revision="0c7526e8ea70" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>