Mercurial > repos > iuc > mothur_biom_info
annotate biom.info.xml @ 6:223e748e0268 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author | iuc |
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date | Tue, 08 Dec 2020 14:00:48 +0000 |
parents | c664838f087c |
children | 458d9a13d2f5 |
rev | line source |
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0
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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1 <tool profile="16.07" id="mothur_biom_info" name="Biom.info" version="@WRAPPER_VERSION@.0"> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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2 <description>create shared and taxonomy files from biom</description> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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3 <macros> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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4 <import>macros.xml</import> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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5 </macros> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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6 <expand macro="requirements"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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7 <expand macro="stdio"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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8 <expand macro="version_command"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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9 <command><![CDATA[ |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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10 @SHELL_OPTIONS@ |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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11 |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 ln -s '$biom' input.biom && |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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13 |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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14 echo 'biom.info( |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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15 biom=input.biom, |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 #if str($label) != '': |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 label=$label, |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 #end if |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 basis=$basis, |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 output=$output, |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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21 relabund=$relabund, |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 printlevel=$printlevel |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 )' |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 | sed 's/ //g' ## mothur trips over whitespace |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 | mothur |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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26 | tee mothur.out.log |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 ]]></command> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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28 <inputs> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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29 <param argument="biom" type="data" format="biom1" label="Biom input dataset"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 <!-- TODO: read label options from biom file --> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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31 <param argument="label" type="text" value="userLabel" label="label - OTU Labels" |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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32 help="Enter a distance label to be used in the shared file created from your biom file (e.g. 0.03)"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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33 <param argument="basis" type="select" label="Summary type" |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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34 help="indicate what you want the summary file to represent, options are otu and sequence. Default is otu. |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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35 For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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36 number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7, |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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37 where 7 is the number of otus that classified to Clostridiales. "> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 <option value="otu" selected="true">OTU</option> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 <option value="sequence">Sequence</option> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 </param> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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41 <param argument="relabund" type="boolean" truevalue="T" falsevalue="F" label="Relative abundance values" |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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42 help="use relative abundances rather than raw abundances for the tax.summary file"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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43 <expand macro="param-output"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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44 <expand macro="param-printlevel"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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45 <expand macro="param-savelog"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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46 </inputs> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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47 <outputs> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 <expand macro="logfile-output"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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49 <data name="shared" format="mothur.shared" from_work_dir="input*.shared" label="${tool.name} on ${on_string}: shared"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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50 <data name="taxonomy" format="mothur.cons.taxonomy" from_work_dir="input*.cons.taxonomy" label="${tool.name} on ${on_string}: cons.taxonomy"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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51 <data name="tax.summary" format="mothur.tax.summary" from_work_dir="input*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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52 </outputs> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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53 <tests> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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54 <test><!-- test with biom without metadata --> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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55 <param name="biom" value="samplebiom.biom1"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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56 <output name="shared" ftype="mothur.shared"> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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57 <assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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58 <expand macro="test-shared-format"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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59 </assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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60 </output> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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61 <param name="savelog" value="true"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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62 <expand macro="logfile-test"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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63 </test> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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64 <test><!-- test with biom file with metadata --> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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65 <param name="biom" value="example.biom"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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66 <output name="shared" ftype="mothur.shared"> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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67 <assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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68 <expand macro="test-shared-format"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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69 </assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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70 </output> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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71 <output name="taxonomy" ftype="mothur.cons.taxonomy"> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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72 <assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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73 <expand macro="test-taxonomy-format"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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74 <has_text text="GG_OTU_1"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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75 </assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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76 </output> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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77 <output name="tax.summary" ftype="mothur.tax.summary"> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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78 <assert_contents> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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79 <expand macro="test-taxsummary-format"/> |
c664838f087c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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80 </assert_contents> |
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81 </output> |
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82 <param name="savelog" value="true"/> |
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83 <expand macro="logfile-test"/> |
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84 </test> |
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85 <test><!-- test with some more parameters --> |
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86 <param name="biom" value="example.biom"/> |
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87 <param name="label" value="0.03"/> |
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88 <param name="output" value="detail"/> |
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89 <param name="basis" value="sequence"/> |
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90 <param name="printlevel" value="4"/> |
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91 <output name="shared" ftype="mothur.shared"> |
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92 <assert_contents> |
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93 <expand macro="test-shared-format"/> |
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94 </assert_contents> |
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95 </output> |
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96 <output name="taxonomy" ftype="mothur.cons.taxonomy"> |
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97 <assert_contents> |
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98 <expand macro="test-taxonomy-format"/> |
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99 <has_text text="GG_OTU_1"/> |
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100 </assert_contents> |
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101 </output> |
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102 <output name="tax.summary" ftype="mothur.tax.summary"> |
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103 <assert_contents> |
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104 <expand macro="test-taxsummary-format"/> |
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105 <has_text text="Euryarchaeota"/> |
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106 </assert_contents> |
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107 </output> |
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108 <param name="savelog" value="true"/> |
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109 <expand macro="logfile-test"/> |
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110 </test> |
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111 </tests> |
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112 <help><![CDATA[ |
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113 |
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114 @MOTHUR_OVERVIEW@ |
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115 |
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116 **Command Documentation** |
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117 |
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118 The biom.info command reads a biom file creates a shared file. If your biom file contains metadata mothur will also |
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119 create taxonomy or constaxonomy along with tax.summary files. |
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120 |
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121 ]]></help> |
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122 <expand macro="citations"/> |
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123 </tool> |