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comparison metastats.xml @ 0:7c817f668dac 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 05:19:54 -0400
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children ce49a6e10308
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-1:000000000000 0:7c817f668dac
1 <tool profile="16.07" id="mothur_metastats" name="Metastats" version="@WRAPPER_VERSION@.0">
2 <description>generate principle components plot data</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 "$otu" otu.dat &&
14 ln -s "$design" design.dat &&
15
16 echo 'metastats(
17 shared=otu.dat,
18 design=design.dat,
19 #if $label:
20 label=${ str($label).replace(",","-") },
21 #end if
22 #if $groups:
23 groups=${ str($groups).replace(",","-") },
24 #end if
25 #if $sets:
26 sets=${ str($sets).replace(",","-") },
27 #end if
28 iters=$iters,
29 threshold=$threshold,
30 processors='\${GALAXY_SLOTS:-8}'
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 | tee mothur.out.log
35 ]]></command>
36 <inputs>
37 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
38 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
40 <expand macro="labeloptions"/>
41 </param>
42 <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
43 <options>
44 <filter type="data_meta" ref="design" key="groups"/>
45 </options>
46 </param>
47 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
48 <options>
49 <filter type="data_meta" ref="otu" key="groups"/>
50 </options>
51 </param>
52 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/>
53 <param name="threshold" type="float" value="0.05" min="0" max="1" label="threshold - significance level to reject null hypotheses"/>
54 </inputs>
55 <outputs>
56 <expand macro="logfile-output"/>
57 <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats">
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/>
59 </collection>
60 </outputs>
61 <tests>
62 <test>
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
64 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
65 <output_collection name="metastats" count="36">
66 <element name="0.23.tardis-dalek" ftype="txt">
67 <assert_contents>
68 <has_text text="group1"/>
69 <has_text text="group2"/>
70 <has_text text="OTU"/>
71 <has_text text="variance"/>
72 <has_text text="1000 permutations"/>
73 </assert_contents>
74 </element>
75 </output_collection>
76 <expand macro="logfile-test"/>
77 </test>
78 <test>
79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
80 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
81 <param name="iters" value="42"/>
82 <param name="threshold" value="0.1"/>
83 <param name="label" value="0.03,0.05,0.23"/>
84 <param name="groups" value="forest,pasture"/>
85 <param name="sets" value="tardis,dalek"/>
86 <output_collection name="metastats" count="3">
87 <element name="0.23.tardis-dalek" ftype="txt">
88 <assert_contents>
89 <has_text text="group1"/>
90 <has_text text="group2"/>
91 <has_text text="OTU"/>
92 <has_text text="variance"/>
93 <has_text text="42 permutations"/>
94 </assert_contents>
95 </element>
96 </output_collection>
97 <expand macro="logfile-test"/>
98 </test>
99 </tests>
100 <help>
101 <![CDATA[
102
103 @MOTHUR_OVERVIEW@
104
105 **Command Documentation**
106
107 The metastats_ command generate principle components plot data.
108
109 .. _metastats: https://www.mothur.org/wiki/Metastats
110
111 v.1.21.0: Updated to mothur 1.33
112 ]]>
113 </help>
114 <expand macro="citations"/>
115 </tool>