# HG changeset patch
# User galaxyp
# Date 1557904691 14400
# Node ID dff7df6fcab54854395a9462781e3c2512aefdf0
# Parent  cd22452edec2d116e4bc5e79153a5a38f1f52d4f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

diff -r cd22452edec2 -r dff7df6fcab5 filter_by_fasta_ids.py
--- a/filter_by_fasta_ids.py	Thu Apr 18 02:45:18 2019 -0400
+++ b/filter_by_fasta_ids.py	Wed May 15 03:18:11 2019 -0400
@@ -61,11 +61,11 @@
     parser.add_argument('-d', help='Path to discarded entries file')
     header_criteria = parser.add_mutually_exclusive_group()
     header_criteria.add_argument('--id_list', help='Path to the ID list file')
-    parser.add_argument('--pattern', help='regex earch attern for ID in FASTA entry')
+    parser.add_argument('--pattern', help='regex search pattern for ID in FASTA entry')
     header_criteria.add_argument('--header_regexp', help='Regular expression pattern the header should match')
     sequence_criteria = parser.add_mutually_exclusive_group()
     sequence_criteria.add_argument('--min_length', type=int, help='Minimum sequence length')
-    sequence_criteria.add_argument('--sequence_regexp', help='Regular expression pattern the header should match')
+    sequence_criteria.add_argument('--sequence_regexp', help='Regular expression pattern the sequence should match')
     parser.add_argument('--max_length', type=int, help='Maximum sequence length')
     parser.add_argument('--dedup', action='store_true', default=False, help='Whether to remove duplicate sequences')
     options = parser.parse_args()
@@ -89,10 +89,10 @@
         work_summary['duplicates'] = 0
 
     if options.id_list:
-        targets = []
+        targets = set()
         with open(options.id_list) as f_target:
             for line in f_target:
-                targets.append(line.strip().upper())
+                targets.add(line.strip().upper())
         work_summary['wanted'] = len(targets)
 
     homd_db = FASTAReader_gen(options.i)
diff -r cd22452edec2 -r dff7df6fcab5 filter_by_fasta_ids.xml
--- a/filter_by_fasta_ids.xml	Thu Apr 18 02:45:18 2019 -0400
+++ b/filter_by_fasta_ids.xml	Wed May 15 03:18:11 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.2">
+<tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.3">
     <description>on the headers and/or the sequences</description>
     <macros>
         <xml name="regexp_macro" token_label="Regular expression pattern">