Mercurial > repos > sanbi-uwc > confil
changeset 8:3892ea8ad1ad draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 371cae3aab4e4874410d5bcdc7885908ce765181
author | sanbi-uwc |
---|---|
date | Thu, 07 Mar 2019 08:24:42 -0500 |
parents | 96c8c5cada47 |
children | 3365813ad7f5 |
files | conda/conda_upload.sh confil.egg-info/PKG-INFO confil.egg-info/SOURCES.txt confil.xml confil/__init__.pyc confil/confil.pyc confil/kraken.pyc confil/report.pyc |
diffstat | 8 files changed, 17 insertions(+), 13 deletions(-) [+] |
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--- a/conda/conda_upload.sh Thu Mar 07 07:12:34 2019 -0500 +++ b/conda/conda_upload.sh Thu Mar 07 08:24:42 2019 -0500 @@ -2,12 +2,9 @@ # Only need to change these two variables PKG_NAME=confil USER=thoba - OS=$TRAVIS_OS_NAME-64 conda config --set anaconda_upload no -DEV='dev' -DATE=`date +%Y%m%d` export CONDA_BLD_PATH=$HOME/miniconda/conda-bld conda build . anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER $CONDA_BLD_PATH/$OS/$PKG_NAME-*.tar.bz2 --force
--- a/confil.egg-info/PKG-INFO Thu Mar 07 07:12:34 2019 -0500 +++ b/confil.egg-info/PKG-INFO Thu Mar 07 08:24:42 2019 -0500 @@ -1,9 +1,12 @@ -Metadata-Version: 2.1 +Metadata-Version: 1.0 Name: confil -Version: 0.1.3.dev20190307 +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) @@ -33,4 +36,3 @@ Keywords: contamination,filter Platform: UNKNOWN -Description-Content-Type: text/markdown
--- a/confil.egg-info/SOURCES.txt Thu Mar 07 07:12:34 2019 -0500 +++ b/confil.egg-info/SOURCES.txt Thu Mar 07 08:24:42 2019 -0500 @@ -3,10 +3,13 @@ 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 Thu Mar 07 07:12:34 2019 -0500 +++ b/confil.xml Thu Mar 07 08:24:42 2019 -0500 @@ -1,21 +1,24 @@ -<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy0"> +<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy1"> <macros> - <token name="@VERSION@">0.1.3</token> + <token name="@VERSION@">0.1.3</token> </macros> <requirements> <requirement type="package" version="@VERSION@">confil</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + ln -s \$(which kraken2) \$(pwd)/kraken2 && + PATH=\$(pwd):\$PATH && export PATH && + #set $input_type = $input_type_conditional.input_type #import re - + ####### Single Input #if $input_type == "single" ln -s "${input_type_conditional.single_input}" $input_type_conditional.single_input.element_identifier && #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' - confil --threads $threads --cutoff $cutoff + 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' @@ -27,7 +30,7 @@ #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 $threads --cutoff $cutoff --paired + confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier && mv $report_name '$output_report' && ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward' @@ -48,8 +51,7 @@ <param name="collection_input" format="fq,fastq,fastq.gz,fastqsanger" type="data_collection" collection_type="paired" label="Select Dataset Pair" help="Specify paired dataset collection containing paired reads" /> </when> </conditional> - <param name="cutoff" type="integer" label="Cutoff percentage" value="50" min="50" max="99" /> - <param name="threads" type="integer" label="Number of threads" value="1" min="1" max="4" /> + <param name="cutoff" type="integer" label="Cutoff percentage" value="90" min="50" max="99" /> </inputs> <outputs> <data name="output_report" format="tabular" label="Kraken2 report" />