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annotate canu.xml @ 0:7d87a6450883 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/canu commit b1d1a13639aff19178a1b521a476a179c39948cc-dirty
author jdv
date Wed, 06 Sep 2017 12:24:44 -0400
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children ed5df116fad3
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7d87a6450883 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/canu commit b1d1a13639aff19178a1b521a476a179c39948cc-dirty
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1 <tool id="canu" name="Canu" version="1.6">
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3 <description>Assembler optimized for long error-prone reads</description>
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5 <!-- ***************************************************************** -->
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7 <!--
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8 <requirements>
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9 <requirement type="package" version="1.6">canu</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>canu --version | perl -wnE'print "$1\n" for /^Canu (?:snapshot v)?(\S+)/g'</version_command>
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18 <!-- ***************************************************************** -->
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20 <command detect_errors="aggressive">
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21 <![CDATA[
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23 canu
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25 -p canu_galaxy
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26 -d out_dir
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27 useGrid=false
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28 genomeSize=$genome_size
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29 rawErrorRate=$raw_error_rate
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30 correctedErrorRate=$corrected_error_rate
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31 minReadLength=$min_read_length
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32 minOverlapLength=$min_overlap
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33 minThreads=\${GALAXY_SLOTS:-1}
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34 maxThreads=\${GALAXY_SLOTS:-1}
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35 gnuplotTested=true
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36 useGrid=false
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37 $mode
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38 $input
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41 ]]>
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42 </command>
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44 <!-- ***************************************************************** -->
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46 <inputs>
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48 <param name="input" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Input reads" />
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49 <param name="mode" type="select">
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50 <option value="-nanopore-raw" selected="true">nanopore raw</option>
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51 <option value="-pacbio-raw">pacbio raw</option>
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52 <option value="-nanopore-corrected">nanopore corrected</option>
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53 <option value="-pacbio-corrected">pacbio corrected</option>
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54 </param>
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55 <param name="genome_size" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" />
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56 <param name="raw_error_rate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
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57 <param name="corrected_error_rate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" />
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58 <param name="min_read_length" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
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59 <param name="min_overlap" type="integer" value="500" min="1" size="5" label="Minimum overlap" />
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61 </inputs>
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63 <!-- ***************************************************************** -->
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65 <outputs>
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67 <data name="contigs" format="fasta" from_work_dir="out_dir/canu_galaxy.contigs.fasta" label="${tool.name} on ${on_string} (contigs)" />
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68 <data name="unitigs" format="fasta" from_work_dir="out_dir/canu_galaxy.unitigs.fasta" label="${tool.name} on ${on_string} (unitigs)" />
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70 </outputs>
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72 <!-- ***************************************************************** -->
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74 <!--
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75 <tests>
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76 <test>
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77 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
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78 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
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79 </test>
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80 </tests>
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81 -->
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83 <!-- ***************************************************************** -->
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85 <help>
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86 <![CDATA[
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88 **Description**
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90 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
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91 sequencing data. Nanopolish can calculate an improved consensus sequence for a
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92 draft genome assembly, detect base modifications, call SNPs and indels with
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93 respect to a reference genome and more.
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94
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95 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
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96 as input, such as can be produced by `poretools combine`, and always outputs a
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97 single FASTQ file.
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98
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99 This is the `extract` module.
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100
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101 ]]>
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102 </help>
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103
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104 <!-- ***************************************************************** -->
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105
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106 <citations>
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107 </citations>
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108
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109 </tool>