Mercurial > repos > iuc > ont_fast5_api_fast5_subset
changeset 0:eb1f4aa80c72 draft
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
| author | iuc |
|---|---|
| date | Mon, 08 Jun 2020 15:57:10 -0400 |
| parents | |
| children | 3bdd8fa109b1 |
| files | fast5_subset.xml macros.xml test-data/batch.fast5 test-data/list.txt |
| diffstat | 4 files changed, 115 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fast5_subset.xml Mon Jun 08 15:57:10 2020 -0400 @@ -0,0 +1,81 @@ +<?xml version="1.0"?> +<tool id="ont_fast5_api_fast5_subset" name="Fast5 subset" version="@TOOL_VERSION@+galaxy0" profile="18.01"> + <description>of multi read file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command></version_command> + <command detect_errors="exit_code"><![CDATA[ +## initialize +mkdir data && +#for $num, $current in enumerate($input): + ln -s '$current' './data/batch${num}.fast5' && +#end for + +## run +fast5_subset +## required +--input ./data +-s ./results +--read_id_list '$read_id_list' +## optional +--batch_size $batch_size +-t \${GALAXY_SLOTS:-4} + ]]></command> + <inputs> + <param argument="--input" type="data" format="fast5" multiple="true" + label="Select multi read input file(s)"/> + <param argument="--read_id_list" type="data" format="tabular" + label="Select file with read_ids" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/> + <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"/> + </inputs> + <outputs> + <data name="out_results" format="fast5"> + <discover_datasets pattern="(?P<designation>.+)\.fast5" format="fast5" directory="results" assign_primary_output="true" visible="true"/> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="batch.fast5"/> + <param name="read_id_list" value="list.txt"/> + <param name="batch_size" value="2"/> + <output name="out_results"> + <assert_contents> + <has_size value="23304"/> + </assert_contents> + <!-- batch0 is represented by out_results --> + <discovered_dataset designation="batch1" ftype="fast5"> + <assert_contents> + <has_size value="17328"/> + </assert_contents> + </discovered_dataset> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +@WID@ + +fast5_subset extracts reads from multi_read_fast5_file(s) based on a list of read IDs. + +**Input** + +A multi read file in FAST5 format and a list of read IDs that should be extracted. + +**Output** + +A multi read file in FAST5 format containing a subset of the input file. + +.. class:: infomark + +**References** + +@REFERENCES@ + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 08 15:57:10 2020 -0400 @@ -0,0 +1,31 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">3.1.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</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> + </xml> + <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