Mercurial > repos > peterjc > seq_filter_by_id

changeset 8:2d4537dbf0bc draft

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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(-) [+]
line wrap: on
line diff
--- 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>