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comparison macros.xml @ 2:ce2bf68a260d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
author iuc
date Thu, 18 Jun 2020 05:08:40 -0400
parents 92cdc29a8620
children 148f32860445
comparison
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1:92cdc29a8620 2:ce2bf68a260d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.0.1</token> 3 <token name="@TOOL_VERSION@">1.0.3</token>
4 <token name="@PROFILE@">18.01</token> 4 <token name="@PROFILE@">18.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
8 </requirements> 8 </requirements>
53 <option value="r941_min_fast_g303">r941_min_fast_g303</option> 53 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
54 <option value="r941_min_high_g303">r941_min_high_g303</option> 54 <option value="r941_min_high_g303">r941_min_high_g303</option>
55 <option value="r941_min_high_g330">r941_min_high_g330</option> 55 <option value="r941_min_high_g330">r941_min_high_g330</option>
56 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option> 56 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
57 <option value="r941_min_high_g344">r941_min_high_g344</option> 57 <option value="r941_min_high_g344">r941_min_high_g344</option>
58 <option value="r941_min_high_g351" selected="true">r941_min_high_g351</option> 58 <option value="r941_min_high_g351">r941_min_high_g351</option>
59 <option value="r941_min_high_g360">r941_min_high_g360</option> 59 <option value="r941_min_high_g360">r941_min_high_g360</option>
60 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option> 60 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
61 <option value="r941_prom_high_g303">r941_prom_high_g303</option> 61 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
62 <option value="r941_prom_high_g330">r941_prom_high_g330</option> 62 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
63 <option value="r941_prom_high_g344">r941_prom_high_g344</option> 63 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
64 <option value="r941_prom_high_g360">r941_prom_high_g360</option> 64 <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option>
65 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option> 65 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
66 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option> 66 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
67 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option> 67 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
68 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option> 68 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
69 </param> 69 </param>
75 <option value="history">Use a genome from history</option> 75 <option value="history">Use a genome from history</option>
76 </param> 76 </param>
77 <when value="cached"> 77 <when value="cached">
78 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> 78 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
79 <options from_data_table="all_fasta"> 79 <options from_data_table="all_fasta">
80 <filter type="sort_by" column="2" /> 80 <filter type="sort_by" column="2"/>
81 <validator type="no_options" message="No reference genomes are available" /> 81 <validator type="no_options" message="No reference genomes are available"/>
82 </options> 82 </options>
83 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 83 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
84 </param> 84 </param>
85 </when> 85 </when>
86 <when value="history"> 86 <when value="history">
87 <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" /> 87 <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"/>
88 </when> 88 </when>
89 </conditional> 89 </conditional>
90 </xml> 90 </xml>
91 91
92 <!-- 92 <!--
93 Help 93 Help
94 --> 94 -->
95 95
96 <token name="@WID@"><![CDATA[ 96 <token name="@WID@"><![CDATA[
97 medaka is a tool suite to create a consensus sequence from nanopore sequencing data. 97 *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
98 98
99 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. 99 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.
100 ]]></token> 100 ]]></token>
101 <token name="@REFERENCES@"><![CDATA[ 101 <token name="@REFERENCES@"><![CDATA[
102 More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_. 102 More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.