Mercurial > repos > iuc > mothur_classify_tree

comparison classify.tree.xml @ 3:cf0f6c79bd1b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:11:18 -0400
parents 813305556713
children
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2:813305556713 3:cf0f6c79bd1b
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 "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$group" group.dat && 15 ln -s '$group' group.dat &&
16 ln -s "$taxonomy" taxonomy.dat && 16 ln -s '$taxonomy' taxonomy.dat &&
17 17
18 echo 'classify.tree( 18 echo 'classify.tree(
19 tree=tree.dat, 19 tree=tree.dat,
20 #if $name 20 #if $name
21 name=name.dat, 21 name=name.dat,
22 #end if 22 #end if
23 #if $group: 23 #if $group:
24 group=group.dat, 24 group=group.dat,
25 #end if 25 #end if
26 taxonomy=taxonomy.dat 26 taxonomy=taxonomy.dat
27 )' 27 )'
28 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur 29 | mothur
30 | tee mothur.out.log 30 | tee mothur.out.log
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> 33 <param argument="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
34 <param name="tree" type="data" format="txt" label="tree - Sequences to filter"/> 34 <param argument="tree" type="data" format="txt" label="tree - Sequences to filter"/>
35 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/> 35 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
36 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/> 36 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/>
37 <param name="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold" help="The default is 51, meaning 51%. Cutoff cannot be below 51"/> 37 <param argument="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold"
38 help="The default is 51, meaning 51%. Cutoff cannot be below 51"/>
39 <expand macro="param-savelog"/>
38 </inputs> 40 </inputs>
39 <outputs> 41 <outputs>
40 <expand macro="logfile-output"/> 42 <expand macro="logfile-output"/>
41 <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/> 43 <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/>
42 <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/> 44 <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/>
45 <test> 47 <test>
46 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/> 48 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/>
47 <param name="tree" value="treetest.tre" ftype="txt"/> 49 <param name="tree" value="treetest.tre" ftype="txt"/>
48 <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/> 50 <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
49 <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/> 51 <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
52 <param name="savelog" value="true"/>
50 <expand macro="logfile-test"/> 53 <expand macro="logfile-test"/>
51 </test> 54 </test>
52 </tests> 55 </tests>
53 <help> 56 <help><![CDATA[
54 <![CDATA[
55 57
56 @MOTHUR_OVERVIEW@ 58 @MOTHUR_OVERVIEW@
57 59
58 60
59 **Command Documentation** 61 **Command Documentation**
74 .. _name: https://www.mothur.org/wiki/Name_file 76 .. _name: https://www.mothur.org/wiki/Name_file
75 .. _group: https://www.mothur.org/wiki/Group_file 77 .. _group: https://www.mothur.org/wiki/Group_file
76 .. _classify.tree: https://www.mothur.org/wiki/Classify.tree 78 .. _classify.tree: https://www.mothur.org/wiki/Classify.tree
77 79
78 v.1.25.0: Trivial upgrade to Mothur 1.33 80 v.1.25.0: Trivial upgrade to Mothur 1.33
79 ]]> 81
80 </help> 82 ]]></help>
81 <expand macro="citations"/> 83 <expand macro="citations"/>
82 </tool> 84 </tool>