Mercurial > repos > peterjc > samtools_depad
changeset 12:cf3c85c72c57 draft default tip
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty
| author | peterjc |
|---|---|
| date | Fri, 22 Feb 2019 10:20:43 -0500 |
| parents | eb899753409f |
| children | |
| files | tools/samtools_depad/samtools_depad.py tools/samtools_depad/tool_dependencies.xml |
| diffstat | 2 files changed, 17 insertions(+), 6 deletions(-) [+] |
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--- a/tools/samtools_depad/samtools_depad.py Fri Nov 09 11:02:23 2018 -0500 +++ b/tools/samtools_depad/samtools_depad.py Fri Feb 22 10:20:43 2019 -0500 @@ -22,7 +22,10 @@ sys.exit(os.system(cmd)) if len(sys.argv) != 5: - sys.exit("Require four arguments: padded FASTA, SAM/BAM file, format (SAM or BAM), output BAM filenames") + sys.exit( + "Require four arguments: padded FASTA, SAM/BAM file, format " + "(SAM or BAM), output BAM filenames" + ) padded_ref, bam_filename, input_format, output_filename = sys.argv[1:] @@ -35,9 +38,17 @@ # Run samtools depad: if input_format.lower() == "sam": - cmd = "samtools depad -S -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename) + cmd = "samtools depad -S -T '%s' '%s' > '%s'" % ( + padded_ref, + bam_filename, + output_filename, + ) else: - cmd = "samtools depad -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename) + cmd = "samtools depad -T '%s' '%s' > '%s'" % ( + padded_ref, + bam_filename, + output_filename, + ) return_code = os.system(cmd) if return_code:
--- a/tools/samtools_depad/tool_dependencies.xml Fri Nov 09 11:02:23 2018 -0500 +++ b/tools/samtools_depad/tool_dependencies.xml Fri Feb 22 10:20:43 2019 -0500 @@ -1,6 +1,6 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file