Mercurial > repos > iuc > mothur_remove_otulabels

comparison remove.otulabels.xml @ 0:afd434bb48af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:41:35 -0400
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1 <tool profile="16.07" id="mothur_remove_otulabels" name="Remove.otulabels" version="@WRAPPER_VERSION@.0">
2 <description>Removes OTU labels</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 "$infile.otu" infile.otu.dat &&
14 ln -s "$accnos" accnos.dat &&
15
16 echo 'remove.otulabels(
17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
18 constaxonomy=infile.otu.data,
19 #end if
20 #if $infile.otu.is_of_type("mothur.otu.corr"):
21 otucorr=infile.otu.dat,
22 #end if
23 #if $infile.otu.is_of_type("mothur.axes"):
24 corraxes=infile.otu.dat,
25 #end if
26 #if $infile.otu.is_of_type("mothur.list"):
27 list=infile.otu.dat,
28 #end if
29 #if $infile.otu.is_of_type("mothur.shared"):
30 shared=infile.otu.dat,
31 #end if
32 #if $infile.intype == "in_shared" and $infile.label:
33 label=${ str($infile.label).replace(",","-") },
34 #end if
35 accnos=accnos.dat
36 )'
37 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur
39 | tee mothur.out.log
40 ]]></command>
41 <inputs>
42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
43 <conditional name="infile">
44 <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
45 <option value="in_shared">Shared or List file</option>
46 <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
47 </param>
48 <when value="in_shared">
49 <param name="otu" type="data" format="mothur.list,mothur.shared" label="shared/list - allows you to input a list file you wish to select OTUs from. "/>
50 <param name="label" type="select" label="label - pick (one) OTU Label" optional="true" help="By default first label in your file is used">
51 <expand macro="labeloptions"/>
52 </param>
53 </when>
54 <when value="in_other">
55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
56 </when>
57 </conditional>
58 </inputs>
59 <outputs>
60 <expand macro="logfile-output"/>
61 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
62 </outputs>
63 <tests>
64 <test><!-- test with shared/list input and label selection -->
65 <param name="accnos" value="amazon.accnos.otulabels"/>
66 <param name="intype" value="in_shared"/>
67 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
68 <param name="label" value="0.22"/>
69 <output name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/>
70 <expand macro="logfile-test"/>
71 </test>
72 <test><!-- test with constaxonomy/otucorr/corraxes file -->
73 <param name="accnos" value="amazon.accnos.otulabels"/>
74 <param name="intype" value="in_other"/>
75 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
76 <output name="pick_out" md5="9bffef40bf6e879737835cf7323c5ce4" ftype="mothur.axes"/>
77 <expand macro="logfile-test"/>
78 </test>
79 </tests>
80 <help>
81 <![CDATA[
82
83 @MOTHUR_OVERVIEW@
84
85 **Command Documentation**
86
87 The remove.otulabels_ command removes 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.
88
89 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
90 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
91 .. _otu.association: https://www.mothur.org/wiki/Otu.association
92 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
93 ]]>
94 </help>
95 <expand macro="citations"/>
96 </tool>