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comparison diamond_makedb.xml @ 6:64be1ac21109 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author bgruening
date Thu, 27 Sep 2018 06:30:30 -0400
parents df7738595640
children 62c9df8382c2
comparison
equal deleted inserted replaced
5:3c6b132b154a 6:64be1ac21109
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 10
11 <command> 11 <command>
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($tax_cond.tax_select) == 'yes':
20 --taxonmap '$tax_cond.taxonmap'
21 --taxonnodes '$tax_cond.taxonnodes'
22 #end if
23 ]]>
19 </command> 24 </command>
20 25
21 <inputs> 26 <inputs>
22 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" /> 27 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
28 <conditional name="tax_cond">
29 <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner">
30 <option value="yes">Yes</option>
31 <option value="no" selected="true">No</option>
32 </param>
33 <when value="yes">
34 <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" />
35 <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" />
36 </when>
37 <when value="no"/>
38 </conditional>
23 </inputs> 39 </inputs>
24 40
25 <outputs> 41 <outputs>
26 <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/> 42 <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
27 </outputs> 43 </outputs>
28 44
29 <tests> 45 <tests>
30 <test> 46 <test>
31 <param name="infile" value="db.fasta" ftype="fasta"/> 47 <param name="infile" value="db.fasta" ftype="fasta"/>
32 <output name="outfile" value="db.dmnd"/> 48 <output name="outfile" value="db.dmnd" compare="sim_size" delta="2"/>
49 </test>
50 <test>
51 <param name="infile" value="db.fasta" ftype="fasta"/>
52 <conditional name="tax_cond">
53 <param name="tax_select" value="yes"/>
54 <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" />
55 <param name="taxonnodes" ftype="tabular" value="nodes.dmp" />
56 </conditional>
57 <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/>
33 </test> 58 </test>
34 </tests> 59 </tests>
35 60
36 <help> 61 <help>
37 <![CDATA[ 62 <![CDATA[
46 times faster than BLASTX, finding more than 94% of all matches. 71 times faster than BLASTX, finding more than 94% of all matches.
47 72
48 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ 73 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
49 74
50 75
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://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
77
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://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
51 ]]> 79 ]]>
52 </help> 80 </help>
53 81
54 <expand macro="citations" /> 82 <expand macro="citations" />
55 </tool> 83 </tool>