Mercurial > repos > iuc > mothur_list_otulabels

comparison list.otulabels.xml @ 2:88e8819fb923 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 22:16:21 -0400
parents e86c535cf4d1
children e643cc6c39cb
comparison
equal deleted inserted replaced
1:bb8a0eec1872 2:88e8819fb923
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 "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 14
15 echo 'list.otulabels( 15 echo 'list.otulabels(
16 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
17 relabund=otu.dat 17 relabund=otu.dat
18 #elif $otu.is_of_type("mothur.shared"): 18 #elif $otu.is_of_type("mothur.shared"):
19 shared=otu.dat 19 shared=otu.dat
20 #else 20 #else
21 list=otu.dat 21 list=otu.dat
22 #end if 22 #end if
23 #if $label: 23 #if $label:
24 ,label=${ str($label).replace(",","-") } 24 ,label=${ str($label).replace(",","-") }
25 #end if 25 #end if
26 #if $groups: 26 #if $groups:
27 ,groups=${ str($groups).replace(",","-") } 27 ,groups=${ str($groups).replace(",","-") }
28 #end if 28 #end if
29 )' 29 )'
30 | sed 's/ //g' ## mothur trips over whitespace 30 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur 31 | mothur
32 | tee mothur.out.log 32 | tee mothur.out.log
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="otu" type="data" format="mothur.shared,mothur.relabund,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/> 35 <param name="otu" type="data" format="mothur.shared,mothur.relabund,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/>
36 <param name="label" type="select" multiple="true" label="label - OTU Labels"> 36 <param name="label" type="select" multiple="true" label="label - OTU Labels">
37 <expand macro="labeloptions"/> 37 <expand macro="labeloptions"/>
39 <param name="groups" type="select" multiple="true" label="groups - Pairwise comparision groups"> 39 <param name="groups" type="select" multiple="true" label="groups - Pairwise comparision groups">
40 <options> 40 <options>
41 <filter type="data_meta" ref="otu" key="groups"/> 41 <filter type="data_meta" ref="otu" key="groups"/>
42 </options> 42 </options>
43 </param> 43 </param>
44 <expand macro="param-savelog"/>
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <expand macro="logfile-output"/> 47 <expand macro="logfile-output"/>
47 <collection name="otulabels" type="list" label="${tool.name} on ${on_string}: otulabels"> 48 <collection name="otulabels" type="list" label="${tool.name} on ${on_string}: otulabels">
48 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otulabels" format="mothur.otulabels"/> 49 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otulabels" format="mothur.otulabels"/>
54 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 55 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
55 <output_collection name="otulabels" count="36"> 56 <output_collection name="otulabels" count="36">
56 <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/> 57 <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/>
57 <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/> 58 <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/>
58 </output_collection> 59 </output_collection>
60 <param name="savelog" value="true"/>
59 <expand macro="logfile-test"/> 61 <expand macro="logfile-test"/>
60 </test> 62 </test>
61 <test><!-- test with group select --> 63 <test><!-- test with group select -->
62 <param name="infile" value="otulist"/> 64 <param name="infile" value="otulist"/>
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 65 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
64 <param name="groups" value="forest"/> 66 <param name="groups" value="forest"/>
65 <output_collection name="otulabels" count="36"> 67 <output_collection name="otulabels" count="36">
66 <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/> 68 <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/>
67 </output_collection> 69 </output_collection>
70 <param name="savelog" value="true"/>
68 <expand macro="logfile-test"/> 71 <expand macro="logfile-test"/>
69 </test> 72 </test>
70 </tests> 73 </tests>
71 <help> 74 <help><![CDATA[
72 <![CDATA[
73 75
74 @MOTHUR_OVERVIEW@ 76 @MOTHUR_OVERVIEW@
75 77
76 **Command Documentation** 78 **Command Documentation**
77 79
78 The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands. 80 The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otus_ or remove.otulabels_ commands
79 81
80 .. _list.otulabels: https://www.mothur.org/wiki/List.otulabels 82 .. _list.otulabels: https://www.mothur.org/wiki/List.otulabels
81 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu 83 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
82 .. _otu.association: https://www.mothur.org/wiki/Otu.association 84 .. _otu.association: https://www.mothur.org/wiki/Otu.association
83 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes 85 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
86 .. _get.otus: https://www.mothur.org/wiki/Get.otus
84 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels 87 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
85 .. _shared: https://www.mothur.org/wiki/Shared_file 88 .. _shared: https://www.mothur.org/wiki/Shared_file
86 .. _relabund: https://www.mothur.org/wiki/Get.relabund 89 .. _relabund: https://www.mothur.org/wiki/Get.relabund
87 90
88 v.1.27.0: Updated to mothur 1.33, added list file for otu 91 v.1.27.0: Updated to mothur 1.33, added list file for otu
89 ]]> 92
90 </help> 93 ]]></help>
91 <expand macro="citations"/> 94 <expand macro="citations"/>
92 </tool> 95 </tool>