Mercurial > repos > iuc > megan_blast2lca
annotate blast2lca.xml @ 3:a80281b0172e draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
author | iuc |
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date | Sat, 11 Dec 2021 11:53:22 +0000 |
parents | 1930eb870dca |
children |
rev | line source |
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0
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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"
iuc
parents:
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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"
iuc
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3 <macros> |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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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"
iuc
parents:
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5 </macros> |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
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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"
iuc
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9 #import re |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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10 |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
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21 #end if |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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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"
iuc
parents:
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25 #end if |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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26 |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
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27 #set blast_input_identifier = 'blast_input' + $blast_ext |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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28 ln -s '${blast_input}' '${blast_input_identifier}' && |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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29 |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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30 blast2lca |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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31 --input '${blast_input_identifier}' |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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32 --format '${blast_format}' |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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33 --mode '${mode}' |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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44 #if $advanced_options.mapDB: |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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45 --mapDB '$advanced_options.mapDB' |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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46 #end if |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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47 #if $advanced_options.acc2taxa: |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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48 --acc2taxa '$advanced_options.acc2taxa' |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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49 #end if |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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50 #if $advanced_options.syn2taxa: |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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51 --syn2taxa '$advanced_options.syn2taxa' |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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52 #end if |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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53 #if $advanced_options.acc2kegg: |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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54 --acc2kegg '$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"
iuc
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56 #if $advanced_options.syn2kegg: |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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57 --syn2kegg '$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 $advanced_options.firstWordIsAccession |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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60 #if str($advanced_options.accessionTags) != '': |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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"
iuc
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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"/> |
ad69d2a05c3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
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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"
iuc
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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"
iuc
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76 <param argument="--showRanks" type="boolean" truevalue="--showRanks" falsevalue="" checked="true" label="Show taxonomic ranks?"/> |
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77 <param argument="--officialRanksOnly" type="boolean" truevalue="--officialRanksOnly" falsevalue="" checked="true" label="Report only taxa that have an official rank?"/> |
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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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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"/> |
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82 <expand macro="top_percent_param"/> |
0
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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> |
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142 <expand macro="citations"/> |
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143 </tool> |
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144 |