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comparison mash_sketch.xml @ 8:56c1b5f9f8bf draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit e7ac80b7bf62e50eb537b5adbe0a5ece8c4e77df-dirty"
author dfornika
date Mon, 24 Feb 2020 20:42:30 +0000
parents c4182a046647
children
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7:c4182a046647 8:56c1b5f9f8bf
1 <tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01"> 1 <tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01">
2 <description> 2 <description>
3 Create a reduced representation of a sequence or set of sequences, based on min-hashes. 3 Create a reduced representation of a sequence or set of sequences, based on min-hashes
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <expand macro="requirements" />
9 <requirement type="package" version="@TOOL_VERSION@">mash</requirement> 9 <expand macro="version_command" />
10 </requirements>
11 <version_command>mash --version</version_command>
12 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
13 mash sketch 11 mash sketch
14 -s '${sketch_size}' 12 -s '${sketch_size}'
15 -k '${kmer_size}' 13 -k '${kmer_size}'
16 #if str ( $reads_assembly.reads_assembly_selector ) == "reads" 14 #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
61 <when value="assembly"> 59 <when value="assembly">
62 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/> 60 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
63 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/> 61 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/>
64 </when> 62 </when>
65 </conditional> 63 </conditional>
66 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" /> 64 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" />
67 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32"/> 65 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" />
68 </inputs> 66 </inputs>
69 <outputs> 67 <outputs>
70 <data name="sketch" format="msh" from_work_dir="sketch.msh"/> 68 <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
71 </outputs> 69 </outputs>
72 <tests> 70 <tests>
81 <param name="assembly" value="test_assembly.fasta"/> 79 <param name="assembly" value="test_assembly.fasta"/>
82 <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" /> 80 <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" />
83 </test> 81 </test>
84 </tests> 82 </tests>
85 <help><![CDATA[ 83 <help><![CDATA[
86 Description: 84
85 **What it does**
87 86
88 Create a sketch file, which is a reduced representation of a sequence or set 87 Create a sketch file, which is a reduced representation of a sequence or set
89 of sequences (based on min-hashes) that can be used for fast distance 88 of sequences (based on min-hashes) that can be used for fast distance
90 estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can 89 estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can
91 be given to read from standard input. Input files can also be files of file 90 be given to read from standard input. Input files can also be files of file
92 names (see -l). For output, one sketch file will be generated, but it can have 91 names (see -l). For output, one sketch file will be generated, but it can have
93 multiple sketches within it, divided by sequences or files (see -i). By 92 multiple sketches within it, divided by sequences or files (see -i). By
94 default, the output file name will be the first input file with a '.msh' 93 default, the output file name will be the first input file with a '.msh'
95 extension, or 'stdin.msh' if standard input is used (see -o). 94 extension, or 'stdin.msh' if standard input is used (see -o).
96 ]]></help> 95 ]]></help>
97 <citations> 96 <expand macro="citations"/>
98 <citation type="bibtex">
99 @article{ondov2016mash,
100 title={Mash: fast genome and metagenome distance estimation using MinHash},
101 author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
102 journal={Genome biology},
103 volume={17},
104 number={1},
105 pages={132},
106 year={2016},
107 publisher={BioMed Central}
108 }
109 </citation>
110 </citations>
111 </tool> 97 </tool>