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