Mercurial > repos > iuc > megan_blast2lca

annotate blast2lca.xml @ 3:a80281b0172e draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
author iuc
date Sat, 11 Dec 2021 11:53:22 +0000
parents 1930eb870dca
children
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ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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1 <tool id="megan_blast2lca" name="MEGAN Blast2LCA: apply LCA alignment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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2 <description>to produce a taxonomic classification</description>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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3 <macros>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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4 <import>macros.xml</import>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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5 </macros>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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6 <expand macro="bio_tools"/>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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7 <expand macro="requirements"/>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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8 <command detect_errors="exit_code"><![CDATA[
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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9 #import re
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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10
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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11 #if $blast_input.is_of_type('daa'):
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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12 #set blast_format = 'DAA'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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13 #else if $blast_input.is_of_type('txt'):
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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14 #set blast_format = 'BlastText'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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15 #else if $blast_input.is_of_type('blastxml'):
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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16 #set blast_format = 'BlastXML'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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17 #else if $blast_input.is_of_type('tabular'):
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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18 #set blast_format = 'BlastTab'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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19 #else if $blast_input.is_of_type('sam'):
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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20 #set blast_format = 'SAM'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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21 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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22 #set blast_ext = '.' + $blast_format
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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23 #if $blast_input.ext.endswith('.gz'):
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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24 #set blast_ext = $blast_ext + '.gz'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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25 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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26
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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27 #set blast_input_identifier = 'blast_input' + $blast_ext
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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28 ln -s '${blast_input}' '${blast_input_identifier}' &&
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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29
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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30 blast2lca
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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31 --input '${blast_input_identifier}'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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32 --format '${blast_format}'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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33 --mode '${mode}'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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34 $advanced_options.showRanks
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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35 $advanced_options.officialRanksOnly
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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36 $advanced_options.showTaxIds
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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37 --minScore $advanced_options.minScore
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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38 --maxExpected $advanced_options.maxExpected
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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39 --topPercent $advanced_options.topPercent
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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40 --minPercentIdentity $advanced_options.minPercentIdentity
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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41 --maxKeggPerRead $advanced_options.maxKeggPerRead
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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42 $advanced_options.applyTopPercentKegg
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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43 $advanced_options.parseTaxonNames
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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44 #if $advanced_options.mapDB:
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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45 --mapDB '$advanced_options.mapDB'
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46 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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47 #if $advanced_options.acc2taxa:
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48 --acc2taxa '$advanced_options.acc2taxa'
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49 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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50 #if $advanced_options.syn2taxa:
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51 --syn2taxa '$advanced_options.syn2taxa'
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52 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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53 #if $advanced_options.acc2kegg:
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54 --acc2kegg '$advanced_options.acc2kegg'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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55 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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56 #if $advanced_options.syn2kegg:
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57 --syn2kegg '$advanced_options.syn2kegg'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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58 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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59 $advanced_options.firstWordIsAccession
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60 #if str($advanced_options.accessionTags) != '':
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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61 --accessionTags '$advanced_options.maccessionTags'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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62 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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63 #if $advanced_options.kegg:
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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64 --kegg
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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65 --keggOutput '$kegg_output'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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66 #end if
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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67 --output '${taxonomy_output}'
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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68 ]]></command>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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69 <inputs>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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70 <param name="blast_input" argument="--input" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file"/>
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71 <param argument="--mode" type="select" label="Blast mode">
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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72 <expand macro="blast_mode_options"/>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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73 </param>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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74 <section name="advanced_options" title="Advanced options" expanded="false">
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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75 <param argument="--kegg" type="boolean" truevalue="--kegg" falsevalue="" checked="false" label="Map reads to KEGG KOs?"/>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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76 <param argument="--showRanks" type="boolean" truevalue="--showRanks" falsevalue="" checked="true" label="Show taxonomic ranks?"/>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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77 <param argument="--officialRanksOnly" type="boolean" truevalue="--officialRanksOnly" falsevalue="" checked="true" label="Report only taxa that have an official rank?"/>
ad69d2a05c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
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78 <param argument="--showTaxIds" type="boolean" truevalue="--showTaxIds" falsevalue="" checked="false" label="Report taxon ids rather than taxon names?"/>
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a80281b0172e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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79 <expand macro="min_score_param"/>
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80 <expand macro="max_expected_param"/>
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81 <expand macro="min_percent_identity_param"/>
a80281b0172e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
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82 <expand macro="top_percent_param"/>
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83 <param argument="--maxKeggPerRead" type="integer" value="4" label="Maximum number of KEGG assignments to report for a read"/>
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84 <param argument="--applyTopPercentKegg" type="boolean" truevalue="--applyTopPercentKegg" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/>
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85 <param argument="--parseTaxonNames" type="boolean" truevalue="--parseTaxonNames" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/>
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86 <expand macro="mapdb_param"/>
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87 <param argument="--acc2taxa" type="data" format="sqlite" optional="true" label="Accession-to-Taxonomy mapping file"/>
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88 <param argument="--syn2taxa" type="data" format="sqlite" optional="true" label="Synonyms-to-Taxonomy mapping file"/>
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89 <param argument="--acc2kegg" type="data" format="sqlite" optional="true" label="Accession-to-KEGG mapping file"/>
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90 <param argument="--syn2kegg" type="data" format="sqlite" optional="true" label="Synonyms-to-KEGG mapping file"/>
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91 <param argument="--firstWordIsAccession" type="boolean" truevalue="--firstWordIsAccession" falsevalue="" checked="true" label="First word in reference header is accession number?" help="Set to true for NCBI-nr downloaded Sep 2016 or later"/>
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92 <param argument="--accessionTags" type="text" optional="true" label="List of accession tags" help="Specify a space-separated list of tags (e.g., 'gb|' 'ref|')">
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93 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
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94 </param>
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95 </section>
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96 </inputs>
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97 <outputs>
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98 <data name="taxonomy_output" format="txt"/>
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99 <data name="kegg_output" format="txt" label="${tool.name} on ${on_string} (KEGG)">
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100 <filter>advanced_options['kegg']</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <test expect_num_outputs="2">
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105 <param name="blast_input" value="blast_R1.txt" ftype="txt"/>
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106 <param name="mode" value="BlastN"/>
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107 <section name="advanced_options">
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108 <param name="kegg" value="true"/>
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109 </section>
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110 <output name="taxonomy_output" file="taxonomy_output.txt" ftype="txt"/>
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111 <output name="kegg_output" file="kegg_output.txt" ftype="txt"/>
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112 </test>
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113 </tests>
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114 <help>
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115 **What it does**
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116
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117 Applies the LCA alignment to reads and can also perform KEGG classification. The input is a BLAST file or something similar.
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118 This wrapper supports the following formats for the input Blast file. The SAM, Tabular and Text formats can be produced by
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119 The Galaxy MALT Analyzer tool. When these formats are used, this tool will apply the SAM, BlastText and BlastTab format options
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120 required by MEGAN.
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121
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122 * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files
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123 * **BlastXML** - XML output from Blast
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124 * **Sequence Alignment/Map (SAM)** - a tab-delimited text format consisting of a header section, which is optional, and an alignment section
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125 * **Tabular** - information presented in the form of a table with rows and columns
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126 * **Text** - plain text format
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127
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128 The tool produces a text file for the LCA alignment.
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129
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130 If the option to Map reads to KEGG KOs is selected, an additional text file containing the KEGG classification is produced.
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131 The KEGG database provides a collection of metabolic pathways and other pathways, but due to KEGG licensing restrictions, the
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132 Community Edition of KEGG (used by this tool) ships with an early 2011 version of the KEGG classification, so KEGG pathways
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133 cannot be viewed in the putput.
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134
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135 The KEGG classification can be displayed as a tree. Genes are mapped onto so-called KO groups and these are present in one or
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136 more pathways. The MEGAN program will attempt to map each read onto a gene that has a valid KO identifier and thus, to one or
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137 more pathways.
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138
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139 To perform this analysis, MEGAN uses a mapping of GI numbers to KO groups. Hence, if a KEGG-based analysis is desired, then
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140 the database that is used in the BLAST alignment must contain GI numbers.
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141 </help>
1
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142 <expand macro="citations"/>
0
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143 </tool>
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144