Mercurial > repos > iuc > mothur_deunique_tree

comparison deunique.tree.xml @ 3:6f140b20e011 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:10:19 -0400
parents 44d01ad18366
children 283af2e6130c
comparison
equal deleted inserted replaced
2:44d01ad18366 3:6f140b20e011
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$tree" tree.dat && 13 ln -s '$tree' tree.dat &&
14 ln -s "$names" names.dat && 14 ln -s '$names' names.dat &&
15 15
16 echo 'deunique.tree( 16 echo 'deunique.tree(
17 tree=tree.dat, 17 tree=tree.dat,
18 name=names.dat 18 name=names.dat
19 )' 19 )'
20 | sed 's/ //g' ## mothur trips over whitespace 20 | sed 's/ //g' ## mothur trips over whitespace
21 | mothur 21 | mothur
22 | tee mothur.out.log 22 | tee mothur.out.log
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="tree" type="data" format="mothur.tre" label="tree - Sequences to filter"/> 25 <param name="tree" type="data" format="mothur.tre" label="tree - Sequences to filter"/>
26 <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/> 26 <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/>
27 <expand macro="param-savelog"/>
27 </inputs> 28 </inputs>
28 <outputs> 29 <outputs>
29 <expand macro="logfile-output"/> 30 <expand macro="logfile-output"/>
30 <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" label="${tool.name} on ${on_string}: deunique.tre"/> 31 <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" label="${tool.name} on ${on_string}: deunique.tre"/>
31 </outputs> 32 </outputs>
32 <tests> 33 <tests>
33 <test> 34 <test>
34 <param name="tree" value="treetest.tre"/> 35 <param name="tree" value="treetest.tre"/>
35 <param name="names" value="treetest.names"/> 36 <param name="names" value="treetest.names"/>
36 <output name="out_tree" file="treetest.deunique.tre"/> 37 <output name="out_tree" file="treetest.deunique.tre"/>
38 <param name="savelog" value="true"/>
37 <expand macro="logfile-test"/> 39 <expand macro="logfile-test"/>
38 </test> 40 </test>
39 </tests> 41 </tests>
40 <help> 42 <help><![CDATA[
41 <![CDATA[
42 43
43 @MOTHUR_OVERVIEW@ 44 @MOTHUR_OVERVIEW@
44 45
45 46
46 **Command Documentation** 47 **Command Documentation**
50 .. _name: https://www.mothur.org/wiki/Name_file 51 .. _name: https://www.mothur.org/wiki/Name_file
51 .. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree 52 .. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree
52 53
53 v1.21.0: Updated to Mothur 1.33 54 v1.21.0: Updated to Mothur 1.33
54 55
55 ]]> 56 ]]></help>
56 </help>
57 <expand macro="citations"/> 57 <expand macro="citations"/>
58 </tool> 58 </tool>