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comparison 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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0:6b86c86eab26 1:15dbb444df71
1 <tool id="hifiasm_meta" name="Hifiasm_meta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> 1 <tool id="hifiasm_meta" name="Hifiasm_meta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>for metagenome assembly using Hifi reads.</description> 2 <description>for metagenome assembly using Hifi reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
19 hifiasm_meta 19 hifiasm_meta
20 --lowq-10 '$read_selection.lowq_10' 20 --lowq-10 '$read_selection.lowq_10'
21 --lowq-3 '$read_selection.lowq_3' 21 --lowq-3 '$read_selection.lowq_3'
22 --lowq-5 '$read_selection.lowq_5' 22 --lowq-5 '$read_selection.lowq_5'
23 -a '$assembly.a' 23 -a '$assembly.a'
24 #if $f:
25 -f '$f'
26 #end if
24 -k '$overlap_correction.k' 27 -k '$overlap_correction.k'
25 -o asm 28 -o asm
26 -r '$overlap_correction.r' 29 -r '$overlap_correction.r'
27 #if '$read_selection.S': 30 $read_selection.S
28 -S
29 #end if
30 -t \${GALAXY_SLOTS:-4} 31 -t \${GALAXY_SLOTS:-4}
31 '$reads_fn' 32 '$reads_fn'
32 33
33 ]]></command> 34 ]]></command>
34 <inputs> 35 <inputs>
35 <!-- fastq files (could be a repeat or a collection) -->
36 <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" /> 36 <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" />
37 <!-- This hidden parameter is only used to save RAM for planemo test. -->
38 <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
39 <param type="hidden" optional="true" argument="-f" />
37 <section name="read_selection" title="Read selection" expanded="false"> 40 <section name="read_selection" title="Read selection" expanded="false">
38 <param argument='-S' type="boolean" checked="true" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." /> 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." />
39 <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." /> 42 <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." />
40 <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." /> 43 <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." />
41 <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." /> 44 <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." />
42 </section> 45 </section>
43 <section name="overlap_correction" title="Overlap/Error correction" expanded="false"> 46 <section name="overlap_correction" title="Overlap/Error correction" expanded="false">
49 </section> 52 </section>
50 </inputs> 53 </inputs>
51 <outputs> 54 <outputs>
52 <!-- contig graph files --> 55 <!-- contig graph files -->
53 <collection name="contig_graphs" type="list" label="hifiasm_meta on ${on_string}: contig graphs"> 56 <collection name="contig_graphs" type="list" label="hifiasm_meta on ${on_string}: contig graphs">
57 <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" />
54 <data name="Alternate contigs" label="Alternate contigs" from_work_dir="asm.a_ctg.gfa" format="gfa2" /> 58 <data name="Alternate contigs" label="Alternate contigs" from_work_dir="asm.a_ctg.gfa" format="gfa2" />
55 <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" />
56 </collection> 59 </collection>
57 <!-- unitig graph files --> 60 <!-- unitig graph files -->
58 <collection name="unitig_graphs" type="list" label="hifiasm_meta on ${on_string}: unitig graphs"> 61 <collection name="unitig_graphs" type="list" label="hifiasm_meta on ${on_string}: unitig graphs">
59 <data name="Raw unitigs" label="Raw unitigs" from_work_dir="asm.r_utg.gfa" format="gfa2" /> 62 <data name="Raw unitigs" label="Raw unitigs" from_work_dir="asm.r_utg.gfa" format="gfa2" />
60 <data name="Processed unitigs" label="Processed unitigs" from_work_dir="asm.p_utg.gfa" format="gfa2" /> 63 <data name="Processed unitigs" label="Processed unitigs" from_work_dir="asm.p_utg.gfa" format="gfa2" />
66 </outputs> 69 </outputs>
67 <tests> 70 <tests>
68 <!-- 01: basic function --> 71 <!-- 01: basic function -->
69 <test> 72 <test>
70 <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" /> 73 <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" />
71 <param name='S' value="False" /> 74 <param name='f' value="0" />
72 <param name='r' value="1" />
73 <output_collection name="contig_graphs" type="list"> 75 <output_collection name="contig_graphs" type="list">
74 <element name="Primary contigs" file="asm.p_ctg.gfa"/> 76 <element name="Primary contigs" file="asm.p_ctg.gfa"/>
75 <element name="Alternate contigs" file="asm.a_ctg.gfa"/> 77 <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
76 </output_collection> 78 </output_collection>
77 </test> 79 </test>
78 </tests> 80 </tests>
79 <help><![CDATA[ 81 <help><![CDATA[
80 hifiasm_meta 82 hifiasm_meta
81 ------------ 83 ------------
82 84
83 de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 85 de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo
86 assembler for PacBio Hifi reads.
84 87
85 88
86 Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio 89 Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio Hifi
87 Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed 90 reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
88 genome. Thus, it is able to keep the haplotype information as much as possible. 91 genome. Thus, it is able to keep the haplotype information as much as
89 The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its 92 possible. The input of hifiasm is the PacBio Hifi reads in fasta/fastq
90 outputs consist of multiple types of assembly graph in GFA format. 93 format, and its outputs consist of multiple types of assembly graph in GFA
94 format.
91 95
92 Hifiasm_meta is a fork of hifiasm. It comes with a read selection module, which 96 Hifiasm_meta is a fork of hifiasm. It comes with a read selection module,
93 enables the assembly of dataset of high redundancy without compromising overall 97 which enables the assembly of dataset of high redundancy without compromising
94 assembly quality, and meta-centric graphcleaning modules. Currently hifiasm_meta 98 overall assembly quality, and meta-centric graphcleaning modules. Currently
95 does not take bining info. 99 hifiasm_meta does not take binning info.
96 100
97 -------------- 101 --------------
98 102
99 hifiasm_meta's home page is 103 hifiasm_meta's home page is
100 `xfengnefx/hifiasm-meta <https://github.com/xfengnefx/hifiasm-meta>`__. 104 `xfengnefx/hifiasm-meta <https://github.com/xfengnefx/hifiasm-meta>`__.
101 105
102 This tool was wrapped by the Galaxy Australia team. 106 This tool was wrapped by the Galaxy Australia team.
103 ]]></help> 107 ]]></help>
108 <expand macro="citations"/>
104 </tool> 109 </tool>