Mercurial > repos > iuc > mothur_deunique_tree
comparison deunique.tree.xml @ 0:90796e3ff3ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:28:47 -0400 |
| parents | |
| children | 44d01ad18366 |
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| -1:000000000000 | 0:90796e3ff3ef |
|---|---|
| 1 <tool profile="16.07" id="mothur_deunique_tree" name="Deunique.tree" version="@WRAPPER_VERSION@.0"> | |
| 2 <description>Reinsert the redundant sequence identiers back into a unique tree.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <expand macro="stdio"/> | |
| 8 <expand macro="version_command"/> | |
| 9 <command><![CDATA[ | |
| 10 @SHELL_OPTIONS@ | |
| 11 | |
| 12 ## create symlinks to input datasets | |
| 13 ln -s "$tree" tree.dat && | |
| 14 ln -s "$names" names.dat && | |
| 15 | |
| 16 echo 'deunique.tree( | |
| 17 tree=tree.dat, | |
| 18 name=names.dat | |
| 19 )' | |
| 20 | sed 's/ //g' ## mothur trips over whitespace | |
| 21 | mothur | |
| 22 | tee mothur.out.log | |
| 23 ]]></command> | |
| 24 <inputs> | |
| 25 <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/> | |
| 26 <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <expand macro="logfile-output"/> | |
| 30 <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" label="${tool.name} on ${on_string}: deunique.tre"/> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="tree" value="treetest.tre"/> | |
| 35 <param name="names" value="treetest.names"/> | |
| 36 <output name="out_tree" file="treetest.deunique.tre"/> | |
| 37 <expand macro="logfile-test"/> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help> | |
| 41 <![CDATA[ | |
| 42 | |
| 43 @MOTHUR_OVERVIEW@ | |
| 44 | |
| 45 | |
| 46 **Command Documentation** | |
| 47 | |
| 48 The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file. | |
| 49 | |
| 50 .. _name: https://www.mothur.org/wiki/Name_file | |
| 51 .. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree | |
| 52 | |
| 53 v1.21.0: Updated to Mothur 1.33 | |
| 54 | |
| 55 ]]> | |
| 56 </help> | |
| 57 <expand macro="citations"/> | |
| 58 </tool> |