Mercurial > repos > peterjc > count_roi_variants
changeset 12:2429bebcab13 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 79bbb921cb5aa953f0323accd6c8c293c6e486cf-dirty
| author | peterjc |
|---|---|
| date | Tue, 06 Jun 2017 10:17:51 -0400 |
| parents | cc86a2b3dc8e |
| children | 4554d79f238b |
| files | tools/count_roi_variants/README.rst tools/count_roi_variants/count_roi_variants.py tools/count_roi_variants/count_roi_variants.xml |
| diffstat | 3 files changed, 4 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/count_roi_variants/README.rst Fri May 19 06:19:10 2017 -0400 +++ b/tools/count_roi_variants/README.rst Tue Jun 06 10:17:51 2017 -0400 @@ -83,6 +83,7 @@ v0.0.5 - Fix samtools dependency version inconsistency, using v1.2 now. - 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/count_roi_variants/count_roi_variants.py Fri May 19 06:19:10 2017 -0400 +++ b/tools/count_roi_variants/count_roi_variants.py Tue Jun 06 10:17:51 2017 -0400 @@ -20,7 +20,7 @@ if "-v" in sys.argv or "--version" in sys.argv: # Galaxy seems to invert the order of the two lines - print("BAM coverage statistics v0.0.4 (using samtools)") + print("BAM coverage statistics v0.0.6 (using samtools)") cmd = "samtools 2>&1 | grep -i ^Version" sys.exit(os.system(cmd)) @@ -219,6 +219,7 @@ # Call samtools view, don't need header so no -h added. # Only want mapped reads, thus flag filter -F 4. child = subprocess.Popen(["samtools", "view", "-F", "4", bam_file, region], + universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) for line in child.stdout: assert line[0] != "@", "Got unexpected SAM header line: %s" % line
--- a/tools/count_roi_variants/count_roi_variants.xml Fri May 19 06:19:10 2017 -0400 +++ b/tools/count_roi_variants/count_roi_variants.xml Tue Jun 06 10:17:51 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.5"> +<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.6"> <description>using samtools view</description> <requirements> <requirement type="package" version="1.2">samtools</requirement>