Mercurial > repos > devteam > cuffmerge
changeset 13:cf747d1bd79a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
| author | devteam |
|---|---|
| date | Sun, 19 Feb 2017 12:12:38 -0500 |
| parents | 1707a530e598 |
| children | 6a6717a5f421 |
| files | cuff_macros.xml cuffmerge_wrapper.py cuffmerge_wrapper.xml tool_dependencies.xml |
| diffstat | 4 files changed, 3 insertions(+), 34 deletions(-) [+] |
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--- a/cuff_macros.xml Tue Feb 07 18:39:42 2017 -0500 +++ b/cuff_macros.xml Sun Feb 19 12:12:38 2017 -0500 @@ -8,14 +8,6 @@ </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error" /> - <regex match="Exception" /> - </stdio> - </xml> <xml name="condition_inputs"> <!-- DEFAULT : use BAM/SAM files --> <conditional name="in_type">
--- a/cuffmerge_wrapper.py Tue Feb 07 18:39:42 2017 -0500 +++ b/cuffmerge_wrapper.py Sun Feb 19 12:12:38 2017 -0500 @@ -29,23 +29,6 @@ (options, args) = parser.parse_args() - # output version # of tool - try: - with tempfile.NamedTemporaryFile() as tmp_stdout: - returncode = subprocess.call(args='cuffmerge -v 2>&1', stdout=tmp_stdout, shell=True) - stdout = None - with open(tmp_stdout.name) as tmp_stdout2: - for line in tmp_stdout2: - if line.lower().find('merge_cuff_asms v') >= 0: - stdout = line.strip() - break - if stdout: - sys.stdout.write('%s\n' % stdout) - else: - raise Exception - except: - sys.stdout.write('Could not determine Cuffmerge version\n') - # Set/link to sequence file. if options.use_seq_data: if options.ref_file:
--- a/cuffmerge_wrapper.xml Tue Feb 07 18:39:42 2017 -0500 +++ b/cuffmerge_wrapper.xml Sun Feb 19 12:12:38 2017 -0500 @@ -1,11 +1,11 @@ -<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0"> +<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.1"> <description>merge together several Cufflinks assemblies</description> <macros> <import>cuff_macros.xml</import> </macros> <expand macro="requirements" /> - <expand macro="stdio" /> - <command> + <version_command>cuffmerge -v</version_command> + <command detect_errors="aggressive"> python '$__tool_directory__/cuffmerge_wrapper.py' --num-threads="\${GALAXY_SLOTS:-4}"
--- a/tool_dependencies.xml Tue Feb 07 18:39:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="cufflinks" version="2.2.1"> - <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>