Mercurial > repos > peterjc > coverage_stats
changeset 8:86455d19abb8 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats commit 79bbb921cb5aa953f0323accd6c8c293c6e486cf-dirty
| author | peterjc |
|---|---|
| date | Tue, 06 Jun 2017 10:18:36 -0400 |
| parents | f27732bbfafa |
| children | 1cedf1262a02 |
| files | tools/coverage_stats/README.rst tools/coverage_stats/coverage_stats.py tools/coverage_stats/coverage_stats.xml |
| diffstat | 3 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/tools/coverage_stats/README.rst Fri May 19 06:19:37 2017 -0400 +++ b/tools/coverage_stats/README.rst Tue Jun 06 10:18:36 2017 -0400 @@ -65,6 +65,7 @@ - Report total length and overall mean coverage in stdout. - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). +v0.0.6 - Python 3 compatibility fix. ======= ======================================================================
--- a/tools/coverage_stats/coverage_stats.py Fri May 19 06:19:37 2017 -0400 +++ b/tools/coverage_stats/coverage_stats.py Tue Jun 06 10:18:36 2017 -0400 @@ -24,7 +24,7 @@ if "-v" in sys.argv or "--version" in sys.argv: # Galaxy seems to invert the order of the two lines - print("BAM coverage statistics v0.0.5") + print("BAM coverage statistics v0.0.6") cmd = "samtools 2>&1 | grep -i ^Version" sys.exit(os.system(cmd)) @@ -85,6 +85,7 @@ def samtools_depth_opt_available(): """Determine if samtools depth supports maximum coverage argument.""" child = subprocess.Popen(["samtools", "depth"], + universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # Combined stdout/stderr in case samtools is ever inconsistent output, tmp = child.communicate()
--- a/tools/coverage_stats/coverage_stats.xml Fri May 19 06:19:37 2017 -0400 +++ b/tools/coverage_stats/coverage_stats.xml Tue Jun 06 10:18:36 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="coverage_stats" name="BAM coverage statistics" version="0.0.5"> +<tool id="coverage_stats" name="BAM coverage statistics" version="0.0.6"> <description>using samtools idxstats and depth</description> <requirements> <requirement type="package" version="1.4.1">samtools</requirement>