Mercurial > repos > peterjc > mira4_assembler
changeset 38:cee8f9005e43 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
| author | peterjc |
|---|---|
| date | Wed, 11 Jul 2018 12:35:35 -0400 |
| parents | eeeb21870a73 |
| children | bbf14bb9607b |
| files | tools/mira4_0/mira4.py tools/mira4_0/mira4_bait.py tools/mira4_0/mira4_convert.py tools/mira4_0/mira4_make_bam.py tools/mira4_0/mira4_validator.py tools/mira4_0/repository_dependencies.xml |
| diffstat | 6 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- a/tools/mira4_0/mira4.py Thu May 31 04:30:47 2018 -0400 +++ b/tools/mira4_0/mira4.py Wed Jul 11 12:35:35 2018 -0400 @@ -1,6 +1,5 @@ #!/usr/bin/env python -"""A simple wrapper script to call MIRA and collect its output. -""" +"""A simple wrapper script to call MIRA and collect its output.""" from __future__ import print_function @@ -152,7 +151,7 @@ def collect_output(temp, name, handle): - """Moves files to the output filenames (global variables).""" + """Move files to the output filenames (global variables).""" f = "%s/%s_assembly/%s_d_results" % (temp, name, name) if not os.path.isdir(f): log_manifest(manifest) @@ -207,6 +206,7 @@ def clean_up(temp, name): + """Remove temp files.""" folder = "%s/%s_assembly" % (temp, name) if os.path.isdir(folder): shutil.rmtree(folder)
--- a/tools/mira4_0/mira4_bait.py Thu May 31 04:30:47 2018 -0400 +++ b/tools/mira4_0/mira4_bait.py Wed Jul 11 12:35:35 2018 -0400 @@ -1,6 +1,5 @@ #!/usr/bin/env python -"""A simple wrapper script to call MIRA4's mirabait and collect its output. -""" +"""A simple wrapper script to call MIRA4's mirabait and collect its output.""" from __future__ import print_function @@ -14,7 +13,7 @@ def get_version(mira_binary): - """Run MIRA to find its version number""" + """Run MIRA to find its version number.""" # At the commend line I would use: mira -v | head -n 1 # however there is some pipe error when doing that here. cmd = [mira_binary, "-v"]
--- a/tools/mira4_0/mira4_convert.py Thu May 31 04:30:47 2018 -0400 +++ b/tools/mira4_0/mira4_convert.py Wed Jul 11 12:35:35 2018 -0400 @@ -45,7 +45,7 @@ def get_version(mira_binary): - """Run MIRA to find its version number""" + """Run MIRA to find its version number.""" # At the commend line I would use: mira -v | head -n 1 # however there is some pipe error when doing that here. cmd = [mira_binary, "-v"]
--- a/tools/mira4_0/mira4_make_bam.py Thu May 31 04:30:47 2018 -0400 +++ b/tools/mira4_0/mira4_make_bam.py Wed Jul 11 12:35:35 2018 -0400 @@ -1,6 +1,5 @@ #!/usr/bin/env python -"""Wrapper script using miraconvert & samtools to get BAM from MIRA. -""" +"""Wrapper script using miraconvert & samtools to get BAM from MIRA.""" import os import shutil
--- a/tools/mira4_0/mira4_validator.py Thu May 31 04:30:47 2018 -0400 +++ b/tools/mira4_0/mira4_validator.py Wed Jul 11 12:35:35 2018 -0400 @@ -1,9 +1,11 @@ +"""Python code to validate parameters in the Galaxy XML definition.""" + # Called from the Galaxy Tool XML file # import sys def validate_input(trans, error_map, param_values, page_param_map): - """Validates the min_size/max_size user input, before execution.""" + """Validate the min_size/max_size user input, before execution.""" err_list = [] for read_group in param_values["read_group"]: err = dict()
--- a/tools/mira4_0/repository_dependencies.xml Thu May 31 04:30:47 2018 -0400 +++ b/tools/mira4_0/repository_dependencies.xml Wed Jul 11 12:35:35 2018 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format)."> - <repository changeset_revision="7f01823efdd5" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2bd1f1175fb2" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>