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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
author iuc
date Sun, 16 Feb 2020 22:02:43 +0000
parents 7305a1d87e99
children d9fb7a9bce28
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2:7305a1d87e99 3:6d63b05cfea8
1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" profile="19.01"> 1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" profile="19.01">
2 <description>determines how well query sequences are contained within a pool of sequences</description> 2 <description>determines how well query sequences are contained within a pool of sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements" />
7 <requirement type="package" version="@TOOL_VERSION@">mash</requirement> 7 <expand macro="version_command" />
8 </requirements>
9 <version_command>mash --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 ln -s '$queries' queries.msh && 9 ln -s '$queries' queries.msh &&
12 mash screen 10 mash screen
13 $winner_takes_all 11 $winner_takes_all
14 -i $minimum_identity_to_report 12 -i $minimum_identity_to_report
42 <when value="paired_collection"> 40 <when value="paired_collection">
43 <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 41 <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
44 </when> 42 </when>
45 </conditional> 43 </conditional>
46 <param name="queries" type="data" format="msh" /> 44 <param name="queries" type="data" format="msh" />
47 <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/> 45 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
48 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." /> 46 help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
49 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/> 47 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
48 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
50 </inputs> 49 </inputs>
51 <outputs> 50 <outputs>
52 <data name="output" format="tabular" /> 51 <data name="output" format="tabular" />
53 </outputs> 52 </outputs>
54 <tests> 53 <tests>
71 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> 70 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
72 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> 71 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
73 </test> 72 </test>
74 </tests> 73 </tests>
75 <help><![CDATA[ 74 <help><![CDATA[
76 Description: 75
76 **What it does**
77 77
78 Determine how well query sequences are contained within a pool of sequences. 78 Determine how well query sequences are contained within a pool of sequences.
79 The queries must be formatted as a single Mash sketch file (.msh), created 79 The queries must be formatted as a single Mash sketch file (.msh), created
80 with the `mash sketch` command. The <pool> files can be contigs or reads, in 80 with the `mash sketch` command. The <pool> files can be contigs or reads, in
81 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from 81 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
83 be 6-frame translated if the <queries> are amino acids. The output fields are 83 be 6-frame translated if the <queries> are amino acids. The output fields are
84 [identity, shared-hashes, median-multiplicity, p-value, query-ID, 84 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
85 query-comment], where median-multiplicity is computed for shared hashes, based 85 query-comment], where median-multiplicity is computed for shared hashes, based
86 on the number of observations of those hashes within the pool. 86 on the number of observations of those hashes within the pool.
87 ]]></help> 87 ]]></help>
88 <citations> 88 <expand macro="citations"/>
89 <citation type="bibtex">
90 @article{ondov2016mash,
91 title={Mash: fast genome and metagenome distance estimation using MinHash},
92 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},
93 journal={Genome biology},
94 volume={17},
95 number={1},
96 pages={132},
97 year={2016},
98 publisher={BioMed Central}
99 }
100 </citation>
101 </citations>
102 </tool> 89 </tool>