Mercurial > repos > iuc > mothur_make_lefse
annotate make.lefse.xml @ 6:88be2167f369 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author | iuc |
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date | Mon, 02 Dec 2019 05:39:16 -0500 |
parents | 678c90b43e17 |
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rev | line source |
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d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_make_lefse" name="Make.lefse" version="@WRAPPER_VERSION@.0"> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>create a lefse formatted input file from mothur's output files</description> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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8 <expand macro="version_command"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[ |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11 |
2
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$otu' otu.dat && |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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14 ln -s '$design' design.dat && |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 ln -s '$constaxonomy' constaxonomy.dat && |
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d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 |
2
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 echo 'make.lefse( |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 #if $otu.is_of_type("mothur.relabund"): |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 relabund=otu.dat, |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 #else |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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21 shared=otu.dat, |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 #end if |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 #if $design: |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 design=design.dat, |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 #end if |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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26 #if $constaxonomy: |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 constaxonomy=constaxonomy.dat, |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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28 #end if |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 #if $label: |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 label=${ str($label).replace(",","-") }, |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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31 #end if |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 scale=$scale |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 )' |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 | sed 's/ //g' ## mothur trips over whitespace |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 | mothur |
5e4ee2031e00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 | tee mothur.out.log |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 ]]></command> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <inputs> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used"> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <expand macro="labeloptions"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 </param> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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43 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="constaxonomy - provide a constaxonomy file"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <param name="design" type="data" format="tabular" optional="true" label="design - provide your design file"/> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 <param name="scale" type="select" multiple="false" label="scale - select what scale you would like to use to convert your shared file abundances to relative abundances" help=""> |
d58287720f30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <option value="totalgroup" selected="true">totalgroup</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <option value="totalotu">totalotu</option> |
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48 <option value="averagegroup">averagegroup</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <option value="averageotu">averageotu</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 </param> |
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51 <expand macro="param-savelog"/> |
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52 </inputs> |
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53 <outputs> |
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54 <expand macro="logfile-output"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 <data name="lefse_out" format="tabular" from_work_dir="otu*.lefse" label="${tool.name} on ${on_string}: lefse"/> |
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56 </outputs> |
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57 <tests> |
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58 <test><!-- test with shared file and defaults --> |
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59 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
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60 <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/> |
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61 <param name="savelog" value="true"/> |
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62 <expand macro="logfile-test"/> |
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63 </test> |
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64 <test><!-- test with relabund file --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> |
d58287720f30
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66 <param name="design" value="toymothur.design2" ftype="tabular"/> |
d58287720f30
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67 <param name="label" value="0.18"/> |
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68 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/> |
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69 <param name="savelog" value="true"/> |
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70 <expand macro="logfile-test"/> |
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71 </test> |
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72 </tests> |
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73 <help><![CDATA[ |
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74 |
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75 @MOTHUR_OVERVIEW@ |
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76 |
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77 **Command Documentation** |
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78 |
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79 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files. |
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80 |
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81 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse |
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82 |
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83 ]]></help> |
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84 <expand macro="citations"/> |
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85 </tool> |