Mercurial > repos > iuc > medaka_variant
view macros.xml @ 8:edf6d4003fad draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e0684fe95538cf97b1199ad1072d3da6d1619443"
author | iuc |
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date | Tue, 23 Feb 2021 20:13:39 +0000 |
parents | 2308bc523659 |
children | 43815fa60f3a |
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<?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.0.3</token> <token name="@PROFILE@">18.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">medaka</requirement> <yield /> </requirements> </xml> <xml name="version_command"> <version_command>medaka --version</version_command> </xml> <xml name="citations"> <citations> <citation type="bibtex">@online{medaka, author = {Oxford Nanopore Technologies Ltd.}, title = {medaka}, year = 2020, url = {https://github.com/nanoporetech/medaka}, urldate = {2020-05-06} }</citation> </citations> </xml> <!-- command --> <token name="@REF_FASTA@"><![CDATA[ #if $reference_source.reference_source_selector == 'history': ln -f -s '$reference_source.ref_file' reference.fa && #else: ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if ]]></token> <!-- input --> <xml name="b" token_argument="-b"> <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/> </xml> <xml name="model" token_argument="-m" token_label="Select model"> <param argument="@ARGUMENT@" type="select" label="@LABEL@"> <option value="r10_min_high_g303">r10_min_high_g303</option> <option value="r10_min_high_g340">r10_min_high_g340</option> <option value="r103_min_high_g345">r103_min_high_g345</option> <option value="r103_min_high_g360">r103_min_high_g360</option> <option value="r103_prom_high_g360">r103_prom_high_g360</option> <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option> <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option> <option value="r941_min_fast_g303">r941_min_fast_g303</option> <option value="r941_min_high_g303">r941_min_high_g303</option> <option value="r941_min_high_g330">r941_min_high_g330</option> <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option> <option value="r941_min_high_g344">r941_min_high_g344</option> <option value="r941_min_high_g351">r941_min_high_g351</option> <option value="r941_min_high_g360">r941_min_high_g360</option> <option value="r941_prom_fast_g303">r941_prom_fast_g303</option> <option value="r941_prom_high_g303">r941_prom_high_g303</option> <option value="r941_prom_high_g330">r941_prom_high_g330</option> <option value="r941_prom_high_g344">r941_prom_high_g344</option> <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option> <option value="r941_prom_snp_g303">r941_prom_snp_g303</option> <option value="r941_prom_snp_g322">r941_prom_snp_g322</option> <option value="r941_prom_variant_g303">r941_prom_variant_g303</option> <option value="r941_prom_variant_g322">r941_prom_variant_g322</option> </param> </xml> <xml name="reference"> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> <option value="cached">Use a built-in genome</option> <option value="history">Use a genome from history</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> <options from_data_table="all_fasta"> <filter type="sort_by" column="2"/> <validator type="no_options" message="No reference genomes are available"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> </when> </conditional> </xml> <!-- Help --> <token name="@WID@"><![CDATA[ *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster. ]]></token> <token name="@REFERENCES@"><![CDATA[ More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_. ]]></token> </macros>