Mercurial > repos > sanbi-uwc > confil
changeset 4:eaf51f9aff10 draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
author | sanbi-uwc |
---|---|
date | Mon, 04 Mar 2019 03:28:57 -0500 |
parents | 53a61865e86e |
children | a7b05dd0087d |
files | 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 confil.xml confil/__init__.pyc confil/confil.pyc confil/kraken.pyc confil/report.pyc setup.py |
diffstat | 12 files changed, 78 insertions(+), 17 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil.egg-info/PKG-INFO Mon Mar 04 03:28:57 2019 -0500 @@ -0,0 +1,38 @@ +Metadata-Version: 1.0 +Name: confil +Version: 0.1.2.dev20190304 +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 + + [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil) + [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil) + + :no_entry_sign: :construction: **For in-house use** + + `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff. + + ## Requirements + + - kraken2 + + ## Up and running + + ```sh + $ git clone https://github.com/COMBAT-TB/confil.git + ... + $ cd confil + $ virtualenv envname + $ source envname/bin/activate + $ pip install -r requirements.txt + $ python setup.py install + $ confil --help + $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq + ``` + +Keywords: contamination,filter +Platform: UNKNOWN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil.egg-info/SOURCES.txt Mon Mar 04 03:28:57 2019 -0500 @@ -0,0 +1,15 @@ +README.md +setup.cfg +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil.egg-info/dependency_links.txt Mon Mar 04 03:28:57 2019 -0500 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil.egg-info/entry_points.txt Mon Mar 04 03:28:57 2019 -0500 @@ -0,0 +1,3 @@ +[console_scripts] +confil = confil.confil:confil +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil.egg-info/requires.txt Mon Mar 04 03:28:57 2019 -0500 @@ -0,0 +1,1 @@ +click
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil.egg-info/top_level.txt Mon Mar 04 03:28:57 2019 -0500 @@ -0,0 +1,1 @@ +confil
--- a/confil.xml Wed Feb 27 06:20:05 2019 -0500 +++ b/confil.xml Mon Mar 04 03:28:57 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="confil" name="Contamination Filter (confil)" version="0.1.0"> +<tool id="confil" name="Contamination Filter (confil)" version="0.1.2"> <requirements> <requirement type="package" version="7.0">click</requirement> </requirements> @@ -14,7 +14,8 @@ python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff $input_type_conditional.single_input.element_identifier - && mv $report_name '$output' + && mv $report_name '$output_report' + && ln -sf "${input_type_conditional.single_input}" '$output_file1' ####### Paired Collection #elif $input_type == "paired_collection" @@ -25,7 +26,9 @@ python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff --paired $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier - && mv $report_name '$output' + && mv $report_name '$output_report' + && ln -sf "${input_type_conditional.collection_input.forward}" '$output_file1' + && ln -sf "${input_type_conditional.collection_input.reverse}" '$output_file2' #end if ]]> </command> @@ -46,13 +49,19 @@ <param name="threads" type="integer" label="Number of threads" value="1" min="1" max="4" /> </inputs> <outputs> - <data name="output" format="tabular" label="${tool.name} report" /> + <data name="output_report" format="tabular" label="${tool.name} report" /> + <data name="output_file1" format="fastq" label="${tool.name} report"> + </data> + <data name="output_file2" format="fastq" label="${tool.name} report"> + <filter>input_type_conditional['input_type'] == "paired_collection"</filter> + </data> </outputs> <tests> <test> <param name="single_input" value="seq_1.fastq" /> <param name="input_type" value="single" /> - <output name="output" ftype="tabular" file="seq.tab" /> + <output name="output_report" ftype="tabular" file="seq.tab" /> + <output name="output_file1" ftype="fastq" file="seq_1.fastq" /> </test> <test> <param name="collection_input"> @@ -62,20 +71,13 @@ </collection> </param> <param name="input_type" value="paired_collection" /> - <output name="output" ftype='tabular' file="seq.tab" /> + <output name="output_report" ftype='tabular' file="seq.tab" /> + <output name="output_file1" ftype='fastq' file="seq_1.fastq" /> + <output name="output_file2" ftype='fastq' file="seq_2.fastq" /> </test> </tests> <help><![CDATA[ - Usage: confil [OPTIONS] SEQFILES... - -Options: - --db PATH Name for Kraken 2 DB [default: - /tools/databases/kraken2/04092018/standard/; required] - --threads INTEGER Number of threads [default: 1] - --cutoff INTEGER Percentage of fragments covered [default: 90] - --paired The filenames provided have paired-end reads - --help Show this message and exit. - + confil parses a kraken2 report and determines contamination based on a specified cutoff. ]]> </help> <citations> <citation type="bibtex">