changeset 23:0c79302b2c15 draft default tip

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty

--- a/tools/seq_primer_clip/seq_primer_clip.py	Fri Nov 09 11:10:32 2018 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.py	Fri Feb 22 10:25:29 2019 -0500
@@ -53,9 +53,20 @@
 
 # Parse Command Line
 try:
-    in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]
+    (
+        in_file,
+        seq_format,
+        primer_fasta,
+        primer_type,
+        mm,
+        min_len,
+        keep_negatives,
+        out_file,
+    ) = sys.argv[1:]
 except ValueError:
-    sys.exit("Expected 8 arguments, got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv)))
+    sys.exit(
+        "Expected 8 arguments, got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv))
+    )
 
 if in_file == primer_fasta:
     sys.exit("Same file given as both primer sequences and sequences to clip!")
@@ -67,9 +78,13 @@
 try:
     mm = int(mm)
 except ValueError:
-    sys.exit("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)
+    sys.exit(
+        "Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm
+    )
 if mm < 0:
-    sys.exit("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)
+    sys.exit(
+        "Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm
+    )
 if mm not in [0, 1, 2]:
     raise NotImplementedError
 
@@ -86,7 +101,10 @@
 elif keep_negatives.lower() in ["false", "no", "off"]:
     keep_negatives = False
 else:
-    sys.exit("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)
+    sys.exit(
+        "Expected boolean for keep_negatives (e.g. true or false), not %r"
+        % keep_negatives
+    )
 
 
 if primer_type.lower() == "forward":
@@ -150,20 +168,30 @@
         for i, letter in enumerate(seq):
             # We'll use a set to remove any duplicate patterns
             # if letter not in "NX":
-            pattern = seq[:i] + "N" + seq[i + 1:]
-            assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i"
-                                              % (pattern, len(pattern), seq, len(seq)))
+            pattern = seq[:i] + "N" + seq[i + 1 :]
+            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" % (
+                pattern,
+                len(pattern),
+                seq,
+                len(seq),
+            )
             yield make_reg_ex(pattern)
     if mm >= 2:
         for i, letter in enumerate(seq):
             # We'll use a set to remove any duplicate patterns
             # if letter not in "NX":
-            for k, letter in enumerate(seq[i + 1:]):
+            for k, letter in enumerate(seq[i + 1 :]):
                 # We'll use a set to remove any duplicate patterns
                 # if letter not in "NX":
-                pattern = seq[:i] + "N" + seq[i + 1:i + 1 + k] + "N" + seq[i + k + 2:]
-                assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i"
-                                                  % (pattern, len(pattern), seq, len(seq)))
+                pattern = (
+                    seq[:i] + "N" + seq[i + 1 : i + 1 + k] + "N" + seq[i + k + 2 :]
+                )
+                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" % (
+                    pattern,
+                    len(pattern),
+                    seq,
+                    len(seq),
+                )
                 yield make_reg_ex(pattern)
 
 
@@ -204,6 +232,7 @@
 if seq_format.lower() == "sff":
     # SFF is different because we just change the trim points
     if forward:
+
         def process(records):
             global short_clipped, short_neg, clipped, negs
             for record in records:
@@ -226,7 +255,9 @@
                         yield record
                     else:
                         short_neg += 1
+
     else:
+
         def process(records):
             global short_clipped, short_neg, clipped, negs
             for record in records:

--- a/tools/seq_primer_clip/tool_dependencies.xml	Fri Nov 09 11:10:32 2018 -0500
+++ b/tools/seq_primer_clip/tool_dependencies.xml	Fri Feb 22 10:25:29 2019 -0500
@@ -1,9 +1,9 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="biopython" version="1.67">
-        <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
     <package name="galaxy_sequence_utils" version="1.0.1">
-        <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file