| Previous changeset 1:8945bad80f4a (2015-05-13) |
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Commit message:
v0.0.5 Internal changes to command line handling |
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modified:
tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/tool_dependencies.xml |
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| diff -r 8945bad80f4a -r 71afa65f444a tools/samtools_idxstats/README.rst --- a/tools/samtools_idxstats/README.rst Wed May 13 10:35:50 2015 -0400 +++ b/tools/samtools_idxstats/README.rst Tue May 16 09:24:18 2017 -0400 |
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| @@ -54,6 +54,8 @@ v0.0.3 - Embed samtools citation in tool XML. v0.0.4 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.5 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ====================================================================== @@ -68,17 +70,17 @@ 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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ + $ planemo shed_update -t testtoolshed --check_diff tools/samtools_idxstats/ ... or:: - $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ + $ planemo shed_update -t toolshed --check_diff tools/samtools_idxstats/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/samtools_idxstats/ + $ planemo shed_upload --tar_only tools/samtools_idxstats/ ... $ tar -tzf shed_upload.tar.gz test-data/ex1.bam |
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| diff -r 8945bad80f4a -r 71afa65f444a tools/samtools_idxstats/samtools_idxstats.py --- a/tools/samtools_idxstats/samtools_idxstats.py Wed May 13 10:35:50 2015 -0400 +++ b/tools/samtools_idxstats/samtools_idxstats.py Tue May 16 09:24:18 2017 -0400 |
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| @@ -10,35 +10,30 @@ runs "samtools idxstats" and captures the output to the desired tabular file. """ -import sys + import os -import subprocess +import sys import tempfile if "-v" in sys.argv or "--version" in sys.argv: - #Galaxy seems to invert the order of the two lines + # Galaxy seems to invert the order of the two lines print "(Galaxy wrapper v0.0.2)" cmd = "samtools 2>&1 | grep -i ^Version" sys.exit(os.system(cmd)) -def sys_exit(msg, error_level=1): - """Print error message to stdout and quit with given error level.""" - sys.stderr.write("%s\n" % msg) - sys.exit(error_level) - if len(sys.argv) != 4: - sys_exit("Require three arguments: BAM, BAI, tabular filenames") + sys.exit("Require three arguments: BAM, BAI, tabular filenames") bam_filename, bai_filename, tabular_filename = sys.argv[1:] if not os.path.isfile(bam_filename): - sys_exit("Input BAM file not found: %s" % bam_filename) + sys.exit("Input BAM file not found: %s" % bam_filename) if not os.path.isfile(bai_filename): if bai_filename == "None": - sys_exit("Error: Galaxy did not index your BAM file") - sys_exit("Input BAI file not found: %s" % bai_filename) + sys.exit("Error: Galaxy did not index your BAM file") + sys.exit("Input BAI file not found: %s" % bai_filename) -#Assign sensible names with real extensions, and setup symlinks: +# Assign sensible names with real extensions, and setup symlinks: tmp_dir = tempfile.mkdtemp() bam_file = os.path.join(tmp_dir, "temp.bam") bai_file = os.path.join(tmp_dir, "temp.bam.bai") @@ -48,14 +43,14 @@ assert os.path.isfile(bai_file), bai_file assert os.path.isfile(bam_file + ".bai"), bam_file -#Run samtools idxstats: +# Run samtools idxstats: cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename) return_code = os.system(cmd) -#Remove the temp symlinks: +# Remove the temp symlinks: os.remove(bam_file) os.remove(bai_file) os.rmdir(tmp_dir) if return_code: - sys_exit("Return code %i from command:\n%s" % (return_code, cmd)) + sys.exit("Return code %i from command:\n%s" % (return_code, cmd)) |
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| diff -r 8945bad80f4a -r 71afa65f444a tools/samtools_idxstats/samtools_idxstats.xml --- a/tools/samtools_idxstats/samtools_idxstats.xml Wed May 13 10:35:50 2015 -0400 +++ b/tools/samtools_idxstats/samtools_idxstats.xml Tue May 16 09:24:18 2017 -0400 |
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| @@ -1,16 +1,14 @@ -<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4"> +<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.5"> <description>samtools idxstats</description> <requirements> - <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">samtools_idxstats.py --version</version_command> - <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command> + <version_command> +python $__tool_directory__/samtools_idxstats.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/samtools_idxstats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' + </command> <inputs> <param name="input_bam" type="data" format="bam" label="Input BAM file" /> </inputs> |
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| diff -r 8945bad80f4a -r 71afa65f444a tools/samtools_idxstats/tool_dependencies.xml --- a/tools/samtools_idxstats/tool_dependencies.xml Wed May 13 10:35:50 2015 -0400 +++ b/tools/samtools_idxstats/tool_dependencies.xml Tue May 16 09:24:18 2017 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |