| Previous changeset 3:708ce1e5ac94 (2013-11-21) Next changeset 5:530c8d6fedd8 (2017-05-10) |
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Commit message:
v0.0.14 galaxy_sequence_utils dependency etc |
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modified:
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 |
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removed:
test-data/MID4_GLZRM4E04_rnd30.fasta |
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| diff -r 708ce1e5ac94 -r 9b074c1db68e test-data/MID4_GLZRM4E04_rnd30.fasta --- 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 |
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| b'@@ -1,60 +0,0 @@\n->GLZRM4E04IPVGX\n-CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT\n->GLZRM4E04I9EJK\n-CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG\n->GLZRM4E04JHW0A\n-TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC\n->GLZRM4E04IBNFY\n-CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG\n->GLZRM4E04IKCQP\n-CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA\n->GLZRM4E04ITXFU\n-CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT\n->GLZRM4E04JAY4Z\n-CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC\n->GLZRM4E04H9M21\n-CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG\n->GLZRM4E04IQDP5\n-CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG\n->GLZRM4E04I0CYE\n-TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT\n->GLZRM4E04I2NA7\n-CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA\n->GLZRM4E04I5BWJ\n-CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC\n->GLZRM4E04IK8WX\n-GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG\n->GLZRM4E04I22QH\n-CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC\n->GLZRM4E04IVVFA\n-GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG\n->GLZRM4E04ILU3V\n-CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG\n->GLZRM4E04IDVJT\n-CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG\n->GLZRM4E04I3ZJ6\n-CCGACT'..b'AAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG\n->GLZRM4E04I3UBT\n-CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA\n->GLZRM4E04H59S1\n-CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG\n->GLZRM4E04JFA38\n-CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT\n->GLZRM4E04J4EK3\n-CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG\n->GLZRM4E04IK96G\n-CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA\n->GLZRM4E04JVL8Q\n-CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT\n->GLZRM4E04IOQ36\n-CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT\n->GLZRM4E04JBJJ1\n-CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG\n->GLZRM4E04IEFNO\n-CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA\n->GLZRM4E04JOT5I\n-CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG\n->GLZRM4E04J4HNG\n-CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT\n->GLZRM4E04JC544\n-CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC\n' 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| diff -r 708ce1e5ac94 -r 9b074c1db68e test-data/MID4_GLZRM4E04_rnd30.sff |
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| Binary file test-data/MID4_GLZRM4E04_rnd30.sff has changed |
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| diff -r 708ce1e5ac94 -r 9b074c1db68e tools/seq_primer_clip/README.rst --- 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 |
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| @@ -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) |
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| diff -r 708ce1e5ac94 -r 9b074c1db68e tools/seq_primer_clip/seq_primer_clip.py --- 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 |
| [ |
| b'@@ -26,8 +26,8 @@\n (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.\n See accompanying text file for licence details (MIT/BSD style).\n \n-This is version 0.0.8 of the script. Currently it uses Python\'s regular\n-expression engine for finding the primers, which for my needs is fast enough.\n+NOTE: Currently it uses Python\'s regular expression engine for finding the\n+primers, which for my needs is fast enough.\n """\n import sys\n import re\n@@ -35,52 +35,48 @@\n from galaxy_utils.sequence.fastq import fastqReader, fastqWriter\n \n if "-v" in sys.argv or "--version" in sys.argv:\n- print "v0.0.5"\n+ print "v0.0.12"\n sys.exit(0)\n \n-def stop_err(msg, err=1):\n- sys.stderr.write(msg)\n- sys.exit(err)\n-\n try:\n from Bio.Seq import reverse_complement\n from Bio.SeqIO.SffIO import SffIterator, SffWriter\n except ImportError:\n- stop_err("Requires Biopython 1.54 or later")\n+ sys.exit("Requires Biopython 1.54 or later")\n try:\n from Bio.SeqIO.SffIO import ReadRocheXmlManifest\n except ImportError:\n- #Prior to Biopython 1.56 this was a private function\n+ # Prior to Biopython 1.56 this was a private function\n from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest\n \n-#Parse Command Line\n+# Parse Command Line\n try:\n in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]\n except ValueError:\n- stop_err("Expected 8 arguments, got %i:\\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))\n+ sys.exit("Expected 8 arguments, got %i:\\n%s" % (len(sys.argv) - 1, " ".join(sys.argv)))\n \n if in_file == primer_fasta:\n- stop_err("Same file given as both primer sequences and sequences to clip!")\n+ sys.exit("Same file given as both primer sequences and sequences to clip!")\n if in_file == out_file:\n- stop_err("Same file given as both sequences to clip and output!")\n+ sys.exit("Same file given as both sequences to clip and output!")\n if primer_fasta == out_file:\n- stop_err("Same file given as both primer sequences and output!")\n+ sys.exit("Same file given as both primer sequences and output!")\n \n try:\n mm = int(mm)\n except ValueError:\n- stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)\n+ sys.exit("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)\n if mm < 0:\n- stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)\n-if mm not in [0,1,2]:\n+ sys.exit("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)\n+if mm not in [0, 1, 2]:\n raise NotImplementedError\n \n try:\n min_len = int(min_len)\n except ValueError:\n- stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)\n+ sys.exit("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)\n if min_len < 0:\n- stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)\n+ sys.exit("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)\n \n \n if keep_negatives.lower() in ["true", "yes", "on"]:\n@@ -88,7 +84,7 @@\n elif keep_negatives.lower() in ["false", "no", "off"]:\n keep_negatives = False\n else:\n- stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)\n+ sys.exit("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)\n \n \n if primer_type.lower() == "forward":\n@@ -101,7 +97,7 @@\n forward = False\n rc = True\n else:\n- stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)\n+ sys.exit("Expected foward, reverse or reverse-complement not %r" % primer_type)\n \n \n ambiguous_dna_values = {\n@@ -119,9 +115,9 @@\n "H": "ACTMWYH",\n "D": "AGTRWKD",\n "B": "CGTSYKB",\n- "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC]\n+ "X": ".", # faster than [GATCMRWSYKVVHDBXN] or even [GATC]\n "N": ".",\n- }\n+}\n \n ambiguous_dna_re = {'..b' str(record.seq)[left_clip:right_clip].upper()\n result = primer.search(seq)\n if result:\n- #Reverse primer, take everything before it\n- #so move the right clip back\n+ # Reverse primer, take everything before it\n+ # so move the right clip back\n new_len = result.start()\n if new_len >= min_len:\n record.annotations["clip_qual_right"] = left_clip + new_len\n@@ -246,7 +243,7 @@\n yield record\n else:\n short_neg += 1\n- \n+\n in_handle = open(in_file, "rb")\n try:\n manifest = ReadRocheXmlManifest(in_handle)\n@@ -256,7 +253,7 @@\n out_handle = open(out_file, "wb")\n writer = SffWriter(out_handle, xml=manifest)\n writer.write_file(process(SffIterator(in_handle)))\n- #End of SFF code\n+ # End of SFF code\n elif seq_format.lower().startswith("fastq"):\n in_handle = open(in_file, "rU")\n out_handle = open(out_file, "w")\n@@ -267,7 +264,7 @@\n seq = record.sequence.upper()\n result = primer.search(seq)\n if result:\n- #Forward primer, take everything after it\n+ # Forward primer, take everything after it\n cut = result.end()\n record.sequence = seq[cut:]\n if len(record.sequence) >= min_len:\n@@ -281,13 +278,13 @@\n negs += 1\n writer.write(record)\n else:\n- short_negs += 1\n+ short_neg += 1\n else:\n for record in reader:\n seq = record.sequence.upper()\n result = primer.search(seq)\n if result:\n- #Reverse primer, take everything before it\n+ # Reverse primer, take everything before it\n cut = result.start()\n record.sequence = seq[:cut]\n if len(record.sequence) >= min_len:\n@@ -301,19 +298,19 @@\n negs += 1\n writer.write(record)\n else:\n- short_negs += 1\n-elif seq_format.lower()=="fasta":\n+ short_neg += 1\n+elif seq_format.lower() == "fasta":\n in_handle = open(in_file, "rU")\n out_handle = open(out_file, "w")\n reader = fastaReader(in_handle)\n writer = fastaWriter(out_handle)\n- #Following code is identical to that for FASTQ but without editing qualities\n+ # Following code is identical to that for FASTQ but without editing qualities\n if forward:\n for record in reader:\n seq = record.sequence.upper()\n result = primer.search(seq)\n if result:\n- #Forward primer, take everything after it\n+ # Forward primer, take everything after it\n cut = result.end()\n record.sequence = seq[cut:]\n if len(record.sequence) >= min_len:\n@@ -326,13 +323,13 @@\n negs += 1\n writer.write(record)\n else:\n- short_negs += 1\n+ short_neg += 1\n else:\n for record in reader:\n seq = record.sequence.upper()\n result = primer.search(seq)\n if result:\n- #Reverse primer, take everything before it\n+ # Reverse primer, take everything before it\n cut = result.start()\n record.sequence = seq[:cut]\n if len(record.sequence) >= min_len:\n@@ -345,9 +342,9 @@\n negs += 1\n writer.write(record)\n else:\n- short_negs += 1\n+ short_neg += 1\n else:\n- stop_err("Unsupported file type %r" % seq_format)\n+ sys.exit("Unsupported file type %r" % seq_format)\n in_handle.close()\n out_handle.close()\n \n' |
| b |
| diff -r 708ce1e5ac94 -r 9b074c1db68e tools/seq_primer_clip/seq_primer_clip.xml --- 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 |
| b |
| @@ -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> |
| b |
| diff -r 708ce1e5ac94 -r 9b074c1db68e tools/seq_primer_clip/tool_dependencies.xml --- 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 |
| b |
| @@ -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> |