changeset 4:9b074c1db68e draft

v0.0.14 galaxy_sequence_utils dependency etc
author peterjc
date Thu, 02 Feb 2017 11:52:37 -0500
parents 708ce1e5ac94
children 530c8d6fedd8
files test-data/MID4_GLZRM4E04_rnd30.fasta test-data/MID4_GLZRM4E04_rnd30.sff tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.py tools/seq_primer_clip/seq_primer_clip.xml tools/seq_primer_clip/tool_dependencies.xml
diffstat 6 files changed, 116 insertions(+), 167 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/MID4_GLZRM4E04_rnd30.fasta	Thu Nov 21 10:47:23 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
->GLZRM4E04IPVGX
-CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
->GLZRM4E04I9EJK
-CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
->GLZRM4E04JHW0A
-TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
->GLZRM4E04IBNFY
-CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
->GLZRM4E04IKCQP
-CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
->GLZRM4E04ITXFU
-CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT
->GLZRM4E04JAY4Z
-CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
->GLZRM4E04H9M21
-CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
->GLZRM4E04IQDP5
-CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG
->GLZRM4E04I0CYE
-TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT
->GLZRM4E04I2NA7
-CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
->GLZRM4E04I5BWJ
-CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
->GLZRM4E04IK8WX
-GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG
->GLZRM4E04I22QH
-CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
->GLZRM4E04IVVFA
-GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG
->GLZRM4E04ILU3V
-CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
->GLZRM4E04IDVJT
-CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG
->GLZRM4E04I3ZJ6
-CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
->GLZRM4E04I3UBT
-CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
->GLZRM4E04H59S1
-CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
->GLZRM4E04JFA38
-CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
->GLZRM4E04J4EK3
-CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
->GLZRM4E04IK96G
-CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
->GLZRM4E04JVL8Q
-CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT
->GLZRM4E04IOQ36
-CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
->GLZRM4E04JBJJ1
-CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG
->GLZRM4E04IEFNO
-CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
->GLZRM4E04JOT5I
-CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
->GLZRM4E04J4HNG
-CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT
->GLZRM4E04JC544
-CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
Binary file test-data/MID4_GLZRM4E04_rnd30.sff has changed
--- a/tools/seq_primer_clip/README.rst	Thu Nov 21 10:47:23 2013 -0500
+++ b/tools/seq_primer_clip/README.rst	Thu Feb 02 11:52:37 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
 ===========================================================
 
-This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -23,18 +23,19 @@
 
 There are just two files to install:
 
-* seq_primer_clip.py (the Python script)
-* seq_primer_clip.xml (the Galaxy tool definition)
+* ``seq_primer_clip.py`` (the Python script)
+* ``seq_primer_clip.xml`` (the Galaxy tool definition)
 
-The suggested location is a new tools/seq_primer_clip folder. You will also
-need to modify the tools_conf.xml file to tell Galaxy to offer the tool::
+The suggested location is a new ``tools/seq_primer_clip/`` folder. You will
+also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
+tool::
 
   <tool file="seq_primer_clip/seq_primer_clip.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id seq_primer_clip
+    $ ./run_tests.sh -id seq_primer_clip
 
 You will also need to install Biopython 1.54 or later. That's it.
 
@@ -62,6 +63,14 @@
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
 v0.0.11 - Correct automated dependency definition.
+v0.0.12 - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
+v0.0.13 - Use ``format_source=...`` tag.
+        - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Fixed input file help text.
+v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed).
+        - Explicit dependency on ``galaxy_sequence_utils``.
 ======= ======================================================================
 
 
@@ -75,19 +84,24 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
 
-    $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/tool_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30*
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-Check this worked::
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    ...
 
-    $ tar -tzf seq_primer_clip.tar.gz
-    tools/seq_primer_clip/README.rst
-    tools/seq_primer_clip/seq_primer_clip.xml
-    tools/seq_primer_clip/seq_primer_clip.py
-    tools/seq_primer_clip/tool_dependencies.xml
-    test-data/dop_primers.fasta
+or::
+
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_primer_clip/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
     test-data/MID4_GLZRM4E04_rnd30.fasta
     test-data/MID4_GLZRM4E04_rnd30.fastqsanger
     test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
@@ -97,6 +111,11 @@
     test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
     test-data/MID4_GLZRM4E04_rnd30_frclip.sff
     test-data/MID4_GLZRM4E04_rnd30.sff
+    test-data/dop_primers.fasta
+    tools/seq_primer_clip/README.rst
+    tools/seq_primer_clip/seq_primer_clip.py
+    tools/seq_primer_clip/seq_primer_clip.xml
+    tools/seq_primer_clip/tool_dependencies.xml
 
 
 Licence (MIT)
--- a/tools/seq_primer_clip/seq_primer_clip.py	Thu Nov 21 10:47:23 2013 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.py	Thu Feb 02 11:52:37 2017 -0500
@@ -26,8 +26,8 @@
 (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
 See accompanying text file for licence details (MIT/BSD style).
 
-This is version 0.0.8 of the script. Currently it uses Python's regular
-expression engine for finding the primers, which for my needs is fast enough.
+NOTE: Currently it uses Python's regular expression engine for finding the
+primers, which for my needs is fast enough.
 """
 import sys
 import re
@@ -35,52 +35,48 @@
 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.5"
+    print "v0.0.12"
     sys.exit(0)
 
-def stop_err(msg, err=1):
-    sys.stderr.write(msg)
-    sys.exit(err)
-
 try:
     from Bio.Seq import reverse_complement
     from Bio.SeqIO.SffIO import SffIterator, SffWriter
 except ImportError:
-    stop_err("Requires Biopython 1.54 or later")
+    sys.exit("Requires Biopython 1.54 or later")
 try:
     from Bio.SeqIO.SffIO import ReadRocheXmlManifest
 except ImportError:
-    #Prior to Biopython 1.56 this was a private function
+    # Prior to Biopython 1.56 this was a private function
     from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
 
-#Parse Command Line
+# Parse Command Line
 try:
     in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]
 except ValueError:
-    stop_err("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:
-    stop_err("Same file given as both primer sequences and sequences to clip!")
+    sys.exit("Same file given as both primer sequences and sequences to clip!")
 if in_file == out_file:
-    stop_err("Same file given as both sequences to clip and output!")
+    sys.exit("Same file given as both sequences to clip and output!")
 if primer_fasta == out_file:
-    stop_err("Same file given as both primer sequences and output!")
+    sys.exit("Same file given as both primer sequences and output!")
 
 try:
     mm = int(mm)
 except ValueError:
-    stop_err("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:
-    stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)
-if mm not in [0,1,2]:
+    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
 
 try:
     min_len = int(min_len)
 except ValueError:
-    stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)
+    sys.exit("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)
 if min_len < 0:
-    stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)
+    sys.exit("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)
 
 
 if keep_negatives.lower() in ["true", "yes", "on"]:
@@ -88,7 +84,7 @@
 elif keep_negatives.lower() in ["false", "no", "off"]:
     keep_negatives = False
 else:
-    stop_err("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":
@@ -101,7 +97,7 @@
     forward = False
     rc = True
 else:
-    stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)
+    sys.exit("Expected foward, reverse or reverse-complement not %r" % primer_type)
 
 
 ambiguous_dna_values = {
@@ -119,9 +115,9 @@
     "H": "ACTMWYH",
     "D": "AGTRWKD",
     "B": "CGTSYKB",
-    "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC]
+    "X": ".",  # faster than [GATCMRWSYKVVHDBXN] or even [GATC]
     "N": ".",
-    }
+}
 
 ambiguous_dna_re = {}
 for letter, values in ambiguous_dna_values.iteritems():
@@ -134,39 +130,41 @@
 def make_reg_ex(seq):
     return "".join(ambiguous_dna_re[letter] for letter in seq)
 
+
 def make_reg_ex_mm(seq, mm):
     if mm > 2:
         raise NotImplementedError("At most 2 mismatches allowed!")
     seq = seq.upper()
     yield make_reg_ex(seq)
-    for i in range(1,mm+1):
-        #Missing first/last i bases at very start/end of sequence
-        for reg in make_reg_ex_mm(seq[i:],  mm-i):
+    for i in range(1, mm + 1):
+        # Missing first/last i bases at very start/end of sequence
+        for reg in make_reg_ex_mm(seq[i:], mm - i):
             yield "^" + reg
-        for reg in make_reg_ex_mm(seq[:-i], mm-i):
+        for reg in make_reg_ex_mm(seq[:-i], mm - i):
             yield "$" + reg
     if mm >= 1:
-        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:]
+        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))
             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:]):
-                #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:]
+    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:]):
+                # 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))
                 yield make_reg_ex(pattern)
 
+
 def load_primers_as_re(primer_fasta, mm, rc=False):
-    #Read primer file and record all specified sequences
+    # Read primer file and record all specified sequences
     primers = set()
     in_handle = open(primer_fasta, "rU")
     reader = fastaReader(in_handle)
@@ -176,19 +174,18 @@
             seq = reverse_complement(record.sequence)
         else:
             seq = record.sequence
-        #primers.add(re.compile(make_reg_ex(seq)))
+        # primers.add(re.compile(make_reg_ex(seq)))
         count += 1
         for pattern in make_reg_ex_mm(seq, mm):
             primers.add(pattern)
     in_handle.close()
-    #Use set to avoid duplicates, sort to have longest first
-    #(so more specific primers found before less specific ones)
+    # Use set to avoid duplicates, sort to have longest first
+    # (so more specific primers found before less specific ones)
     primers = sorted(set(primers), key=lambda p: -len(p))
-    return count, re.compile("|".join(primers)) #make one monster re!
+    return count, re.compile("|".join(primers))  # make one monster re!
 
 
-
-#Read primer file and record all specified sequences
+# Read primer file and record all specified sequences
 count, primer = load_primers_as_re(primer_fasta, mm, rc)
 print "%i primer sequences" % count
 
@@ -197,8 +194,8 @@
 clipped = 0
 negs = 0
 
-if seq_format.lower()=="sff":
-    #SFF is different because we just change the trim points
+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
@@ -208,8 +205,8 @@
                 seq = str(record.seq)[left_clip:right_clip].upper()
                 result = primer.search(seq)
                 if result:
-                    #Forward primer, take everything after it
-                    #so move the left clip along
+                    # Forward primer, take everything after it
+                    # so move the left clip along
                     if len(seq) - result.end() >= min_len:
                         record.annotations["clip_qual_left"] = left_clip + result.end()
                         clipped += 1
@@ -231,8 +228,8 @@
                 seq = str(record.seq)[left_clip:right_clip].upper()
                 result = primer.search(seq)
                 if result:
-                    #Reverse primer, take everything before it
-                    #so move the right clip back
+                    # Reverse primer, take everything before it
+                    # so move the right clip back
                     new_len = result.start()
                     if new_len >= min_len:
                         record.annotations["clip_qual_right"] = left_clip + new_len
@@ -246,7 +243,7 @@
                         yield record
                     else:
                         short_neg += 1
-    
+
     in_handle = open(in_file, "rb")
     try:
         manifest = ReadRocheXmlManifest(in_handle)
@@ -256,7 +253,7 @@
     out_handle = open(out_file, "wb")
     writer = SffWriter(out_handle, xml=manifest)
     writer.write_file(process(SffIterator(in_handle)))
-    #End of SFF code
+    # End of SFF code
 elif seq_format.lower().startswith("fastq"):
     in_handle = open(in_file, "rU")
     out_handle = open(out_file, "w")
@@ -267,7 +264,7 @@
             seq = record.sequence.upper()
             result = primer.search(seq)
             if result:
-                #Forward primer, take everything after it
+                # Forward primer, take everything after it
                 cut = result.end()
                 record.sequence = seq[cut:]
                 if len(record.sequence) >= min_len:
@@ -281,13 +278,13 @@
                     negs += 1
                     writer.write(record)
                 else:
-                    short_negs += 1
+                    short_neg += 1
     else:
         for record in reader:
             seq = record.sequence.upper()
             result = primer.search(seq)
             if result:
-                #Reverse primer, take everything before it
+                # Reverse primer, take everything before it
                 cut = result.start()
                 record.sequence = seq[:cut]
                 if len(record.sequence) >= min_len:
@@ -301,19 +298,19 @@
                     negs += 1
                     writer.write(record)
                 else:
-                    short_negs += 1
-elif seq_format.lower()=="fasta":
+                    short_neg += 1
+elif seq_format.lower() == "fasta":
     in_handle = open(in_file, "rU")
     out_handle = open(out_file, "w")
     reader = fastaReader(in_handle)
     writer = fastaWriter(out_handle)
-    #Following code is identical to that for FASTQ but without editing qualities
+    # Following code is identical to that for FASTQ but without editing qualities
     if forward:
         for record in reader:
             seq = record.sequence.upper()
             result = primer.search(seq)
             if result:
-                #Forward primer, take everything after it
+                # Forward primer, take everything after it
                 cut = result.end()
                 record.sequence = seq[cut:]
                 if len(record.sequence) >= min_len:
@@ -326,13 +323,13 @@
                     negs += 1
                     writer.write(record)
                 else:
-                    short_negs += 1
+                    short_neg += 1
     else:
         for record in reader:
             seq = record.sequence.upper()
             result = primer.search(seq)
             if result:
-                #Reverse primer, take everything before it
+                # Reverse primer, take everything before it
                 cut = result.start()
                 record.sequence = seq[:cut]
                 if len(record.sequence) >= min_len:
@@ -345,9 +342,9 @@
                     negs += 1
                     writer.write(record)
                 else:
-                    short_negs += 1
+                    short_neg += 1
 else:
-    stop_err("Unsupported file type %r" % seq_format)
+    sys.exit("Unsupported file type %r" % seq_format)
 in_handle.close()
 out_handle.close()
 
--- a/tools/seq_primer_clip/seq_primer_clip.xml	Thu Nov 21 10:47:23 2013 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Thu Feb 02 11:52:37 2017 -0500
@@ -1,20 +1,21 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
-        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
+    <command interpreter="python">
+seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    </command>
     <inputs>
-        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/>
+        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>
         <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
         <param name="primer_type" type="select" label="Type of primers">
             <option value="Forward">Forward (5') primers</option>
@@ -28,18 +29,7 @@
         <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="data" label="$primer_type primer clipped">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="$primer_type primer clipped"/>
     </outputs>
     <tests>
         <test>
@@ -97,9 +87,6 @@
             <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
         </test>
     </tests>
-    <requirements>
-        <requirement type="python-module">Bio</requirement>
-    </requirements>
     <help>
 
 **What it does**
@@ -140,4 +127,7 @@
 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_primer_clip 
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>
--- a/tools/seq_primer_clip/tool_dependencies.xml	Thu Nov 21 10:47:23 2013 -0500
+++ b/tools/seq_primer_clip/tool_dependencies.xml	Thu Feb 02 11:52:37 2017 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="biopython" version="1.62">
-        <repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://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>
+    <package name="galaxy_sequence_utils" version="1.0.1">
+        <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>