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annotate hifiasm_meta.xml @ 1:15dbb444df71 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta commit 939f7ba1b584cb940244def0b6765d2494af3b94
author iuc
date Wed, 18 Jan 2023 09:12:38 +0000
parents 6b86c86eab26
children fa35f1106d3e
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1 <tool id="hifiasm_meta" name="Hifiasm_meta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>for metagenome assembly using Hifi reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ##################
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9 ## SET UP FILES ##
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10 ##################
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12 #set reads_fn = 'reads.' + $reads.ext
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13 ln -s '$reads' '$reads_fn' &&
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15 #################
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16 ## RUN HIFIASM ##
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17 #################
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19 hifiasm_meta
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20 --lowq-10 '$read_selection.lowq_10'
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21 --lowq-3 '$read_selection.lowq_3'
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22 --lowq-5 '$read_selection.lowq_5'
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23 -a '$assembly.a'
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24 #if $f:
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25 -f '$f'
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26 #end if
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27 -k '$overlap_correction.k'
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28 -o asm
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29 -r '$overlap_correction.r'
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30 $read_selection.S
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31 -t \${GALAXY_SLOTS:-4}
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32 '$reads_fn'
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33
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34 ]]></command>
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35 <inputs>
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36 <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" />
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37 <!-- This hidden parameter is only used to save RAM for planemo test. -->
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38 <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
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39 <param type="hidden" optional="true" argument="-f" />
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40 <section name="read_selection" title="Read selection" expanded="false">
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41 <param argument='-S' type="boolean" checked="true" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." />
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42 <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." />
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43 <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." />
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44 <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." />
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45 </section>
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46 <section name="overlap_correction" title="Overlap/Error correction" expanded="false">
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47 <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" />
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48 <param argument='-r' type="integer" value='3' min="1" max="10" label="rounds of correction" />
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49 </section>
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50 <section name="assembly" title="Assembly" expanded="false">
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51 <param argument='-a' type="integer" value='4' min="1" max="10" label="rounds of assembly cleaning" />
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52 </section>
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53 </inputs>
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54 <outputs>
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55 <!-- contig graph files -->
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56 <collection name="contig_graphs" type="list" label="hifiasm_meta on ${on_string}: contig graphs">
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57 <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" />
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58 <data name="Alternate contigs" label="Alternate contigs" from_work_dir="asm.a_ctg.gfa" format="gfa2" />
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59 </collection>
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60 <!-- unitig graph files -->
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61 <collection name="unitig_graphs" type="list" label="hifiasm_meta on ${on_string}: unitig graphs">
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62 <data name="Raw unitigs" label="Raw unitigs" from_work_dir="asm.r_utg.gfa" format="gfa2" />
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63 <data name="Processed unitigs" label="Processed unitigs" from_work_dir="asm.p_utg.gfa" format="gfa2" />
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64 </collection>
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65 <!-- Simplified graphs for visualisation -->
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66 <collection name="simple_graphs" type="list" label="hifiasm_meta on ${on_string}: graphs for visualisation">
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67 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.noseq.gfa" format="gfa2" visible="false" />
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68 </collection>
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69 </outputs>
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70 <tests>
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71 <!-- 01: basic function -->
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72 <test>
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73 <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" />
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74 <param name='f' value="0" />
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75 <output_collection name="contig_graphs" type="list">
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76 <element name="Primary contigs" file="asm.p_ctg.gfa"/>
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77 <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
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78 </output_collection>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 hifiasm_meta
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83 ------------
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84
1
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85 de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo
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86 assembler for PacBio Hifi reads.
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87
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89 Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio Hifi
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90 reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
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91 genome. Thus, it is able to keep the haplotype information as much as
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92 possible. The input of hifiasm is the PacBio Hifi reads in fasta/fastq
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93 format, and its outputs consist of multiple types of assembly graph in GFA
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94 format.
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96 Hifiasm_meta is a fork of hifiasm. It comes with a read selection module,
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97 which enables the assembly of dataset of high redundancy without compromising
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98 overall assembly quality, and meta-centric graphcleaning modules. Currently
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99 hifiasm_meta does not take binning info.
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101 --------------
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103 hifiasm_meta's home page is
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104 `xfengnefx/hifiasm-meta <https://github.com/xfengnefx/hifiasm-meta>`__.
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105
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106 This tool was wrapped by the Galaxy Australia team.
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107 ]]></help>
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108 <expand macro="citations"/>
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109 </tool>