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Note ahead ========== The Galaxy tool xml files in this repository are generated automatically by: - parsing the python argparse definitions in a single xml file - which is postprocessed into separate tool xml files using prepare.sh Currently this has been tested only for a few tools: - checkm_lineage_wf Feel free to extend the prepare.sh script to get also the other tools functional. Limitations: ============ Checkm accepts nucleotide or aminoacid sequences. For the latter `--gene` needs to be added. Currently checkm checks of the sequences are are really nucleotide or aminoacid sequences, respectively, and asks the user if the choice is correct. This seems to affect tree, analyze, merge https://github.com/Ecogenomics/CheckM/issues/171 As a workaround the Galaxy wrappers do `echo | checkm ...`, ie one enter (which triggers the default answer) is presented to checkm. This aborts the program, but no negative exit code results (ie the result woul look positive .. but it is not). This is covered via stdio regex. At least this way check finishes. Reference data initialisation: ============================== Before the CheckM and the Galaxy tools can be used the reference data needs to be downloaded, extracted and the CheckM needs to be told where you put the data. 1. Download reference data with: `wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz` and extract to a location of your choice. 2. The path to the reference data needs to be set by the galaxy user with: `checkm data setRoot PATH` which stores the PATH: CONDA_ENV_PATHemail@example.com/lib/python2.7/site-packages/checkm/DATA_CONFIG Generation of tool xml files ============================ (paths might differ) ``` git clone https://github.com/erasche/argparse2tool.git cd argparse2tool virtualenv .venv . ./.venv/bin/activate python setup.py PYTHONPATH=/home/berntm/projects/argparse2tool/.venv/lib/python2.7/site-packages/argparse2tool-0.4.4-py2.7.egg export PATH=/home/berntm/miniconda3/bin/:$PATH /home/berntm/miniconda3/bin/conda create -c bioconda -y --name firstname.lastname@example.org checkm-genome=1.0.11 /email@example.com/bin/checkm ``` edit checkm to include only the part relevant for argparse add name to plot_need_qa_results_parser and plot_parser python checkm --generate_galaxy_xml > checkm.xml - manually created - macros.xml - tool_data_table_conf.xml.[sample|test] - added test-data/checkm_references.loc and downloaded checkm reference data - add tool specific tests etc in macros_NAME.xml TODOs ===== - next: taxon_wf taxon_set - replace phylum taxon input by a now select where the options are from the output of checkm taxon_list - add section around plot macros and find a nice order - some tools seem to accept hmm in adition to marker_file as input - there are options with label ==SUPPRESS== that should be removed - add help for hmmer output files: """ The hmmer.tree.txt file is the alignment of the genes used to insert your genome into the CheckM reference tree. These genes are uses solely for this purpose. The hmmer.analyze.txt contains the alignment of the genes used to assess the completeness and contamination of your genomes. """