Mercurial > repos > thanhlv > fastani

comparison fastani.xml @ 0:93549392d20d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastani commit 6410237f37dfd76382f9780e73a14cf48aba3695-dirty
author thanhlv
date Fri, 19 Jul 2019 06:49:02 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:93549392d20d
1 <tool id="fastani" name="FastANI" version="1.1">
2 <description> fast alignment-free computation of whole-genome Average Nucleotide Identity</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <version_command>fastANI --version</version_command>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 #for $counter_q, $input_q in enumerate($query):
11 ln -fs '$input_q' ${input_q.element_identifier}_query &&
12 echo ${input_q.element_identifier}_query >> query.lst &&
13 #end for
14
15 #for $counter_r, $input_r in enumerate($reference):
16 ln -fs '$input_r' ${input_r.element_identifier}_ref &&
17 echo ${input_r.element_identifier}_query >> ref.lst &&
18 #end for
19
20 fastANI
21 #if len($query) == 1 and len($reference) == 1:
22 -q ${input_q.element_identifier}_query -r ${input_r.element_identifier}_ref -o output
23 #elif len($query) == 1 and len($reference) > 1:
24 -q ${input_q.element_identifier}_query --rl ref.lst -o output
25 #elif len($query) > 1 and len($reference) > 1:
26 --ql query.lst --rl ref.lst -o output
27 #end if
28
29 2>&1
30 ]]></command>
31 <inputs>
32 <param name="query" type="data" format="fasta" multiple="true" label="Query sequences" />
33 <param name="reference" type="data" format="fasta" multiple="true" label="Reference sequence" />
34 </inputs>
35 <outputs>
36 <data name="output" format="txt" from_work_dir="output" label="${tool.name} on ${on_string} Output"/>
37 </outputs>
38 <tests>
39 <test>
40 <param name="query" value="Shigella_flexneri_2a_01.fna" />
41 <param name="reference" value="Escherichia_coli_str_K12_MG1655.fna" />
42 <output name="output" file="fastani.out" compare="sim_size" />
43 </test>
44 </tests>
45 <help><![CDATA[
46 FastANI is developed for fast alignment-free computation of whole-genome
47 Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide
48 identity of orthologous gene pairs shared between two microbial genomes.
49 FastANI supports pairwise comparison of both complete and draft genome
50 assemblies. Its underlying procedure follows a similar workflow as described
51 by Goris et al. 2007. However, it avoids expensive sequence alignments and
52 uses Mashmap as its MinHash based sequence mapping engine to compute the
53 orthologous mappings and alignment identity estimates. Based on our
54 experiments with complete and draft genomes, its accuracy is on par with
55 BLAST-based ANI solver and it achieves two to three orders of magnitude
56 speedup. Therefore, it is useful for pairwise ANI computation of large
57 number of genome pairs. More details about its speed, accuracy and potential
58 applications are described here: "High Throughput ANI Analysis of 90K
59 Prokaryotic Genomes Reveals Clear Species Boundaries".
60 ]]></help>
61 <expand macro="citations" />
62 </tool>