Mercurial > repos > bgruening > diamond

comparison diamond_makedb.xml @ 10:1e3323a44643 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
author iuc
date Fri, 22 Apr 2022 13:51:34 +0000
parents f921014aba5a
children
comparison
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9:f921014aba5a 10:1e3323a44643
1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@" profile="19.01"> 1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
2 <description>Build database from a FASTA file</description> 2 <description>Build database from a FASTA file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
30 <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner"> 30 <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner">
31 <option value="yes">Yes</option> 31 <option value="yes">Yes</option>
32 <option value="no" selected="true">No</option> 32 <option value="no" selected="true">No</option>
33 </param> 33 </param>
34 <when value="yes"> 34 <when value="yes">
35 <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" /> 35 <param argument="--taxonmap" type="data" format="tabular"
36 <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" /> 36 label="Protein accession to taxid mapping file"
37 <param argument="--taxonnames" type="data" format="tabular" label="taxonomy names.dmp from NCBI" help="" /> 37 help="Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features.
38 A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored" />
39 <param argument="--taxonnodes" type="data" format="tabular" label="Taxonomy nodes.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
40 <param argument="--taxonnames" type="data" format="tabular" label="Taxonomy names.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
38 </when> 41 </when>
39 <when value="no"/> 42 <when value="no"/>
40 </conditional> 43 </conditional>
41 </inputs> 44 </inputs>
42 45
74 times faster than BLASTX, finding more than 94% of all matches. 77 times faster than BLASTX, finding more than 94% of all matches.
75 78
76 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ 79 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
77 80
78 81
79 - taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz 82 - taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
80 83
81 - taxonnames: Path to the names.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip 84 - taxonnames: Path to the names.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
82 85
83 - taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip 86 - taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
84 ]]> 87 ]]>