Mercurial > repos > iuc > mothur_get_otulabels

comparison get.otulabels.xml @ 2:29769fb14cd2 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 22:19:23 -0400
parents ca0c577f910d
children
comparison
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1:56b4c4b3ce7c 2:29769fb14cd2
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 "$infile.otu" infile.otu.dat && 13 ln -s '$infile.otu' infile.otu.dat &&
14 ln -s "$accnos" accnos.dat && 14 ln -s '$accnos' accnos.dat &&
15 15
16 echo 'get.otulabels( 16 echo 'get.otulabels(
17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"): 17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
18 constaxonomy=infile.otu.dat, 18 constaxonomy=infile.otu.dat,
19 #end if 19 #end if
20 #if $infile.otu.is_of_type("mothur.otu.corr"): 20 #if $infile.otu.is_of_type("mothur.otu.corr"):
21 otucorr=infile.otu.dat, 21 otucorr=infile.otu.dat,
22 #end if 22 #end if
23 #if $infile.otu.is_of_type("mothur.axes"): 23 #if $infile.otu.is_of_type("mothur.axes"):
24 corraxes=infile.otu.dat, 24 corraxes=infile.otu.dat,
25 #end if 25 #end if
26 #if $infile.otu.is_of_type("mothur.list"): 26 #if $infile.otu.is_of_type("mothur.list"):
27 list=infile.otu.dat, 27 list=infile.otu.dat,
28 #end if 28 #end if
29 #if $infile.otu.is_of_type("mothur.shared"): 29 #if $infile.otu.is_of_type("mothur.shared"):
30 shared=infile.otu.dat, 30 shared=infile.otu.dat,
31 #end if 31 #end if
32 #if $infile.intype == "in_shared" and $infile.label: 32 #if $infile.intype == "in_shared" and $infile.label:
33 label=$infile.label, 33 label=$infile.label,
34 #end if 34 #end if
35 accnos=accnos.dat 35 accnos=accnos.dat
36 )' 36 )'
37 | sed 's/ //g' ## mothur trips over whitespace 37 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur 38 | mothur
39 | tee mothur.out.log 39 | tee mothur.out.log
40 ]]></command> 40 ]]></command>
41 <inputs> 41 <inputs>
42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> 42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
43 <conditional name="infile"> 43 <conditional name="infile">
44 <param name="intype" type="select" label="Which type of files will you be supplying?" help=""> 44 <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
53 </when> 53 </when>
54 <when value="in_other"> 54 <when value="in_other">
55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> 55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
56 </when> 56 </when>
57 </conditional> 57 </conditional>
58 <expand macro="param-savelog"/>
58 </inputs> 59 </inputs>
59 <outputs> 60 <outputs>
60 <expand macro="logfile-output"/> 61 <expand macro="logfile-output"/>
61 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/> 62 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
62 </outputs> 63 </outputs>
65 <param name="intype" value="in_shared"/> 66 <param name="intype" value="in_shared"/>
66 <param name="accnos" value="amazon.accnos.otulabels"/> 67 <param name="accnos" value="amazon.accnos.otulabels"/>
67 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
68 <param name="label" value="0.22"/> 69 <param name="label" value="0.22"/>
69 <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/> 70 <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/>
71 <param name="savelog" value="true"/>
70 <expand macro="logfile-test"/> 72 <expand macro="logfile-test"/>
71 </test> 73 </test>
72 <test> 74 <test>
73 <param name="intype" value="in_other"/> 75 <param name="intype" value="in_other"/>
74 <param name="accnos" value="amazon.accnos.otulabels"/> 76 <param name="accnos" value="amazon.accnos.otulabels"/>
75 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> 77 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
76 <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/> 78 <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/>
79 <param name="savelog" value="true"/>
77 <expand macro="logfile-test"/> 80 <expand macro="logfile-test"/>
78 </test> 81 </test>
79 </tests> 82 </tests>
80 <help> 83 <help><![CDATA[
81 <![CDATA[
82 84
83 @MOTHUR_OVERVIEW@ 85 @MOTHUR_OVERVIEW@
84 86
85 87
86 **Command Documentation** 88 **Command Documentation**
87 89
88 The get.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. 90 The get.otulabels command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected.
89 91
90 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu 92 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
91 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes 93 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
92 .. _otu.association: https://www.mothur.org/wiki/Otu.association 94 .. _otu.association: https://www.mothur.org/wiki/Otu.association
93 95
94 v.1.27.0: Added list and shared parameters, updated to Mothur 1.33 96 v.1.27.0: Added list and shared parameters, updated to Mothur 1.33
95 ]]> 97
96 </help> 98 ]]></help>
97 <expand macro="citations"/> 99 <expand macro="citations"/>
98 </tool> 100 </tool>