Mercurial > repos > peterjc > seq_filter_by_id

changeset 30:bc608928a007 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
author peterjc
date Fri, 09 Nov 2018 11:06:32 -0500
parents 735dfff31c1d
children e449c7af4b49
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
diffstat 3 files changed, 9 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/tools/seq_filter_by_id/README.rst	Fri Sep 15 10:29:45 2017 -0400
+++ b/tools/seq_filter_by_id/README.rst	Fri Nov 09 11:06:32 2018 -0500
@@ -76,7 +76,7 @@
 v0.0.8  - Simplified XML to apply input format to output data.
 v0.2.0  - Can supply ID list as a text parameter (instead of in a file)
         - Using ``optparse`` for the Python command line API.
-        - Advanced option to ignore paired read suffices.
+        - Advanced option to ignore paired read suffixes.
         - Updated dependencies to use Biopython 1.64.
 v0.2.1  - Use Biopython instead of Galaxy for FASTQ handling.
         - Tool definition now embeds citation information.
--- a/tools/seq_filter_by_id/seq_filter_by_id.py	Fri Sep 15 10:29:45 2017 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.py	Fri Nov 09 11:06:32 2018 -0500
@@ -19,7 +19,7 @@
 
 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.
+https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
 This script is copyright 2010-2017 by Peter Cock, The James Hutton Institute
 (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
@@ -70,7 +70,7 @@
                   help="How to combined multiple ID columns (UNION or INTERSECTION)")
 parser.add_option("-s", "--suffix", dest="suffix",
                   action="store_true",
-                  help="Ignore pair-read suffices for matching names")
+                  help="Ignore pair-read suffixes for matching names")
 parser.add_option("-v", "--version", dest="version",
                   default=False, action="store_true",
                   help="Show version and quit")
@@ -86,7 +86,7 @@
 out_positive_file = options.output_positive
 out_negative_file = options.output_negative
 logic = options.logic
-drop_suffices = bool(options.suffix)
+drop_suffixes = bool(options.suffix)
 
 if in_file is None or not os.path.isfile(in_file):
     sys.exit("Missing input file: %r" % in_file)
@@ -150,7 +150,7 @@
     return parts[0]
 
 
-if drop_suffices:
+if drop_suffixes:
     def clean_name(name):
         """Remove suffix."""
         name = check_white_space(name)
@@ -244,7 +244,7 @@
 
 
 def crude_fasta_iterator(handle):
-    """Yields tuples, record ID and the full record as a string."""
+    """Parse FASTA file yielding tuples of (name, sequence)."""
     while True:
         line = handle.readline()
         if line == "":
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml	Fri Sep 15 10:29:45 2017 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml	Fri Nov 09 11:06:32 2018 -0500
@@ -74,7 +74,7 @@
             </param>
             <when value="basic" />
             <when value="advanced">
-                <param name="strip_suffix" type="boolean" value="false" label="Remove typical pair read name suffices when matching identifiers?" help="Will remove suffices including Illumina /1 and /2, Roche 454 .f and .r, and assorted Sanger names like .p* and .q*" />
+                <param name="strip_suffix" type="boolean" value="false" label="Remove typical pair read name suffixes when matching identifiers?" help="Will remove suffixes including Illumina /1 and /2, Roche 454 .f and .r, and assorted Sanger names like .p* and .q*" />
             </when>
         </conditional>
     </inputs>
@@ -180,14 +180,14 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 This tool uses Biopython to read and write SFF files, so you may also wish to
 cite the Biopython application note (and Galaxy too of course):
 
 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.
+https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id