Mercurial > repos > sanbi-uwc > confil
changeset 10:2cde7c81c694 draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 036172521321dbafe62e6d72b3a491f4bc4b9dc9-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 08 Mar 2019 12:46:23 -0500 |
| parents | 3365813ad7f5 |
| children | 72cb19a32d8b |
| files | confil.egg-info/PKG-INFO confil.egg-info/SOURCES.txt confil.xml confil/.confil.py.swp confil/__init__.pyc confil/confil.pyc confil/kraken.pyc confil/report.pyc |
| diffstat | 8 files changed, 20 insertions(+), 19 deletions(-) [+] |
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--- a/confil.egg-info/PKG-INFO Fri Mar 08 02:27:28 2019 -0500 +++ b/confil.egg-info/PKG-INFO Fri Mar 08 12:46:23 2019 -0500 @@ -1,12 +1,9 @@ -Metadata-Version: 1.0 +Metadata-Version: 2.1 Name: confil -Version: 0.1.2.dev20190304 +Version: 0.1.3.dev20190307 Summary: Contamination filter Home-page: https://github.com/COMBAT-TB/confil -Author: UNKNOWN -Author-email: UNKNOWN License: UNKNOWN -Description-Content-Type: text/markdown Description: # confil [](https://travis-ci.org/COMBAT-TB/confil) @@ -36,3 +33,4 @@ Keywords: contamination,filter Platform: UNKNOWN +Description-Content-Type: text/markdown
--- a/confil.egg-info/SOURCES.txt Fri Mar 08 02:27:28 2019 -0500 +++ b/confil.egg-info/SOURCES.txt Fri Mar 08 12:46:23 2019 -0500 @@ -3,13 +3,10 @@ setup.py confil/__init__.py confil/confil.py -confil/kraken.py -confil/report.py confil.egg-info/PKG-INFO confil.egg-info/SOURCES.txt confil.egg-info/dependency_links.txt confil.egg-info/entry_points.txt confil.egg-info/requires.txt confil.egg-info/top_level.txt -test/test_report.py test/test_runner.py \ No newline at end of file
--- a/confil.xml Fri Mar 08 02:27:28 2019 -0500 +++ b/confil.xml Fri Mar 08 12:46:23 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy2"> +<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy3"> <macros> <token name="@VERSION@">0.1.3</token> </macros> @@ -16,11 +16,13 @@ #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' - confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff - $input_type_conditional.single_input.element_identifier - && mv $report_name '$output_report' - && ln -sf "${input_type_conditional.single_input}" '$single_output_file' - + if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff + $input_type_conditional.single_input.element_identifier ; + then + ln -sf "${input_type_conditional.single_input}" '$single_output_file' + else + touch '$single_output_file' # failure - make empty file + fi ####### Paired Collection #elif $input_type == "paired_collection" ln -s "${input_type_conditional.collection_input.forward}" $input_type_conditional.collection_input.forward.element_identifier && @@ -28,12 +30,16 @@ #set report_name = os.path.splitext(os.path.basename($input_type_conditional.collection_input.forward.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' - confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired - $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier + if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired + $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier ; + then + ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward' + && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse' + else + touch '$list_output.forward' && touch '$list_output.reverse' # failure - make empty files + fi + #end if && mv $report_name '$output_report' - && ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward' - && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse' - #end if ]]> </command> <inputs>