Mercurial > repos > iuc > mothur_remove_otulabels

comparison remove.otulabels.xml @ 2:a8863051d303 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 22:22:34 -0400
parents afd434bb48af
children 5133ef623148
comparison
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1:08579dd3bf72 2:a8863051d303
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 'remove.otulabels( 16 echo 'remove.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.data, 18 constaxonomy=infile.otu.data,
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 $infile.label:
33 label=${ str($infile.label).replace(",","-") }, 33 label=${ str($infile.label).replace(",","-") },
34 #end if 34 #end if
35 accnos=accnos.dat 35 accnos=accnos.dat
36 )' 36 )'
37 | sed 's/ //g' ## mothur trips over whitespace 37 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur 38 | mothur
39 | tee mothur.out.log 39 | tee mothur.out.log
40 ]]></command> 40 ]]></command>
41 <inputs> 41 <inputs>
42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> 42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
43 <conditional name="infile"> 43 <conditional name="infile">
44 <param name="intype" type="select" label="Which type of files will you be supplying?" help=""> 44 <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
53 </when> 53 </when>
54 <when value="in_other"> 54 <when value="in_other">
55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> 55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
56 </when> 56 </when>
57 </conditional> 57 </conditional>
58 <expand macro="param-savelog"/>
58 </inputs> 59 </inputs>
59 <outputs> 60 <outputs>
60 <expand macro="logfile-output"/> 61 <expand macro="logfile-output"/>
61 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${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>
64 <test><!-- test with shared/list input and label selection --> 65 <test><!-- test with shared/list input and label selection -->
65 <param name="accnos" value="amazon.accnos.otulabels"/> 66 <param name="accnos" value="amazon.accnos.otulabels"/>
66 <param name="intype" value="in_shared"/> 67 <param name="intype" value="in_shared"/>
67 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 68 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
68 <param name="label" value="0.22"/> 69 <param name="label" value="0.22"/>
69 <output name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/> 70 <output name="pick_out" ftype="mothur.list">
71 <assert_contents>
72 <expand macro="test-list-format"/>
73 <has_text text="U68686"/>
74 <has_text text="0.22"/>
75 <not_has_text text="0.03"/>
76 </assert_contents>
77 </output>
78 <param name="savelog" value="true"/>
70 <expand macro="logfile-test"/> 79 <expand macro="logfile-test"/>
71 </test> 80 </test>
72 <test><!-- test with constaxonomy/otucorr/corraxes file --> 81 <test><!-- test with constaxonomy/otucorr/corraxes file -->
73 <param name="accnos" value="amazon.accnos.otulabels"/> 82 <param name="accnos" value="amazon.accnos.otulabels"/>
74 <param name="intype" value="in_other"/> 83 <param name="intype" value="in_other"/>
75 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> 84 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
76 <output name="pick_out" md5="9bffef40bf6e879737835cf7323c5ce4" ftype="mothur.axes"/> 85 <output name="pick_out" ftype="mothur.axes">
86 <assert_contents>
87 <expand macro="test-axes-format"/>
88 <has_text text="U68686"/>
89 </assert_contents>
90 </output>
91 <param name="savelog" value="true"/>
77 <expand macro="logfile-test"/> 92 <expand macro="logfile-test"/>
78 </test> 93 </test>
79 </tests> 94 </tests>
80 <help> 95 <help><![CDATA[
81 <![CDATA[
82 96
83 @MOTHUR_OVERVIEW@ 97 @MOTHUR_OVERVIEW@
84 98
85 **Command Documentation** 99 **Command Documentation**
86 100
88 102
89 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu 103 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
90 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes 104 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
91 .. _otu.association: https://www.mothur.org/wiki/Otu.association 105 .. _otu.association: https://www.mothur.org/wiki/Otu.association
92 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels 106 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
93 ]]> 107
94 </help> 108 ]]></help>
95 <expand macro="citations"/> 109 <expand macro="citations"/>
96 </tool> 110 </tool>