Mercurial > repos > iuc > ont_fast5_api_fast5_subset
diff macros.xml @ 1:3bdd8fa109b1 draft
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
author | iuc |
---|---|
date | Fri, 12 Jun 2020 15:08:23 -0400 |
parents | eb1f4aa80c72 |
children | 0defe443ea04 |
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--- a/macros.xml Mon Jun 08 15:57:10 2020 -0400 +++ b/macros.xml Fri Jun 12 15:08:23 2020 -0400 @@ -1,31 +1,83 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">3.1.3</token> + <token name="@TOOL_NAME@">ont_fast5_api:</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement> + <requirement type="package" version="1.10.5">hdf5</requirement> </requirements> </xml> - <xml name="citations"> - <citations> - <citation type="bibtex">@online{ont_fast5_api, - author = {Oxford Nanopore Technologies }, - title = {ont_fast5_api}, - year = 2020, - url = {https://github.com/nanoporetech/ont_fast5_api}, - urldate = {2020-06-01} - }</citation> - </citations> + + <!-- command --> + <token name="@BATCHSIZE@"><![CDATA[ +--batch_size $batch_size + ]]></token> + <token name="@COMPRESSION@"><![CDATA[ +#if $compression != 'none' + --compression '$compression' +#end if + ]]></token> + <token name="@INITIALIZE@"><![CDATA[ +mkdir -p './data' && +tar -xf '$input_path' -C './data' && + ]]></token> + <token name="@INPUTPATH@"><![CDATA[ +--input_path './data' + ]]></token> + <token name="@SAVEPATH@"><![CDATA[ +--save_path './results' + ]]></token> + <token name="@TARBALL@"><![CDATA[ +&& find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin + ]]></token> + <token name="@THREADS@"><![CDATA[ +--threads \${GALAXY_SLOTS:-4} + ]]></token> + + <!-- input --> + <xml name="input" token_argument="--input_path" token_label="multi"> + <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/> </xml> - <token name="@WID@"><![CDATA[ -ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. + <xml name="batch_size"> + <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/> + </xml> + <xml name="compression"> + <param argument="compression" type="select" label="Select output compression type"> + <yield/> + <option value="vbz_legacy_v0">VBZ legacy v0</option> + <option value="gzip">GZIP</option> + </param> + </xml> -- Concrete implementation of the FAST5 file schema using the generic h5py library -- Plain-english-named methods to interact with and reflect the FAST5 file schema -- Tools to convert between multi_read and single_read formats -- Tools to compress/decompress raw data in files + <!-- output --> + <xml name="output"> + <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/> + </xml> + + <!-- help --> + <token name="@WID@"><![CDATA[ +*ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. + +- concrete implementation of the FAST5 file schema using the generic h5py library +- plain-english-named methods to interact with and reflect the FAST5 file schema +- tools to convert between multi_read and single_read formats +- tools to compress/decompress raw data in files ]]></token> <token name="@REFERENCES@"><![CDATA[ More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_. ]]></token> -</macros> \ No newline at end of file + + <xml name="citations"> + <citations> + <citation type="bibtex"> + @online{ont_fast5_api, + author = {Oxford Nanopore Technologies }, + title = {ont_fast5_api}, + year = 2020, + url = {https://github.com/nanoporetech/ont_fast5_api}, + urldate = {2020-06-01} + }</citation> + </citations> + </xml> +</macros>