| Previous changeset 4:9b074c1db68e (2017-02-02) Next changeset 6:b9dc7c967ee6 (2017-05-16) |
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Commit message:
v0.0.15 - internal changes |
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modified:
tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.py tools/seq_primer_clip/seq_primer_clip.xml |
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| diff -r 9b074c1db68e -r 530c8d6fedd8 tools/seq_primer_clip/README.rst --- a/tools/seq_primer_clip/README.rst Thu Feb 02 11:52:37 2017 -0500 +++ b/tools/seq_primer_clip/README.rst Wed May 10 13:09:52 2017 -0400 |
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| @@ -69,8 +69,10 @@ - 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). +v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. - Explicit dependency on ``galaxy_sequence_utils``. +v0.0.15 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only) ======= ====================================================================== @@ -89,17 +91,17 @@ 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):: - $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ + $ planemo shed_update -t testtoolshed --check_diff tools/seq_primer_clip/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ + $ planemo shed_update -t toolshed --check_diff 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/ + $ planemo shed_upload --tar_only tools/seq_primer_clip/ ... $ tar -tzf shed_upload.tar.gz test-data/MID4_GLZRM4E04_rnd30.fasta |
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| diff -r 9b074c1db68e -r 530c8d6fedd8 tools/seq_primer_clip/seq_primer_clip.py --- a/tools/seq_primer_clip/seq_primer_clip.py Thu Feb 02 11:52:37 2017 -0500 +++ b/tools/seq_primer_clip/seq_primer_clip.py Wed May 10 13:09:52 2017 -0400 |
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| @@ -29,8 +29,10 @@ NOTE: Currently it uses Python's regular expression engine for finding the primers, which for my needs is fast enough. """ + +import re import sys -import re + from galaxy_utils.sequence.fasta import fastaReader, fastaWriter from galaxy_utils.sequence.fastq import fastqReader, fastqWriter @@ -147,8 +149,8 @@ # 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)) + 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): @@ -158,8 +160,8 @@ # 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)) + assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i" + % (pattern, len(pattern), seq, len(seq))) yield make_reg_ex(pattern) |
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| diff -r 9b074c1db68e -r 530c8d6fedd8 tools/seq_primer_clip/seq_primer_clip.xml --- a/tools/seq_primer_clip/seq_primer_clip.xml Thu Feb 02 11:52:37 2017 -0500 +++ b/tools/seq_primer_clip/seq_primer_clip.xml Wed May 10 13:09:52 2017 -0400 |
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| @@ -1,18 +1,14 @@ -<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14"> +<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.15"> <description>Trim off 5' or 3' primers</description> <requirements> <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> - <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 + <version_command> +python $__tool_directory__/seq_primer_clip.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/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" help="FASTA, FASTQ, or SFF format."/> |