Mercurial > repos > bgruening > diamond

comparison diamond_makedb.xml @ 8:54f751e413f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
author iuc
date Mon, 22 Mar 2021 13:21:23 +0000
parents 62c9df8382c2
children f921014aba5a
comparison
equal deleted inserted replaced
7:62c9df8382c2 8:54f751e413f4
6 6
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 10
11 <command> 11 <command detect_errors="aggressive">
12 <!-- DB has two files, *.dmnd and *.tx --> 12 <!-- DB has two files, *.dmnd and *.tx -->
13 <![CDATA[ 13 <![CDATA[
14 diamond makedb 14 diamond makedb
15 --threads "\${GALAXY_SLOTS:-12}" 15 --threads "\${GALAXY_SLOTS:-12}"
16 --in '$infile' 16 --in '$infile'
17 --db ./database 17 --db ./database
18 18
19 #if str($tax_cond.tax_select) == 'yes': 19 #if str($tax_cond.tax_select) == 'yes':
20 --taxonmap '$tax_cond.taxonmap' 20 --taxonmap '$tax_cond.taxonmap'
21 --taxonnodes '$tax_cond.taxonnodes' 21 --taxonnodes '$tax_cond.taxonnodes'
22 --taxonnames '$tax_cond.taxonnames'
22 #end if 23 #end if
23 ]]> 24 ]]>
24 </command> 25 </command>
25 26
26 <inputs> 27 <inputs>
31 <option value="no" selected="true">No</option> 32 <option value="no" selected="true">No</option>
32 </param> 33 </param>
33 <when value="yes"> 34 <when value="yes">
34 <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" /> 35 <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" />
35 <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" /> 36 <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" />
37 <param argument="--taxonnames" type="data" format="tabular" label="taxonomy names.dmp from NCBI" help="" />
36 </when> 38 </when>
37 <when value="no"/> 39 <when value="no"/>
38 </conditional> 40 </conditional>
39 </inputs> 41 </inputs>
40 42
51 <param name="infile" value="db.fasta" ftype="fasta"/> 53 <param name="infile" value="db.fasta" ftype="fasta"/>
52 <conditional name="tax_cond"> 54 <conditional name="tax_cond">
53 <param name="tax_select" value="yes"/> 55 <param name="tax_select" value="yes"/>
54 <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" /> 56 <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" />
55 <param name="taxonnodes" ftype="tabular" value="nodes.dmp" /> 57 <param name="taxonnodes" ftype="tabular" value="nodes.dmp" />
58 <param name="taxonnames" ftype="tabular" value="names.dmp" />
56 </conditional> 59 </conditional>
57 <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/> 60 <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/>
58 </test> 61 </test>
59 </tests> 62 </tests>
60 63
71 times faster than BLASTX, finding more than 94% of all matches. 74 times faster than BLASTX, finding more than 94% of all matches.
72 75
73 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ 76 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
74 77
75 78
76 - 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.gz 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
80
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
77 82
78 - 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 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
79 ]]> 84 ]]>
80 </help> 85 </help>
81 86