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comparison metastats.xml @ 2:ce49a6e10308 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 22:26:03 -0400
parents 7c817f668dac
children 10866c1f8e06
comparison
equal deleted inserted replaced
1:526310931966 2:ce49a6e10308
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 ln -s "$design" design.dat && 14 ln -s '$design' design.dat &&
15 15
16 echo 'metastats( 16 echo 'metastats(
17 shared=otu.dat, 17 shared=otu.dat,
18 design=design.dat, 18 design=design.dat,
19 #if $label: 19 #if $label:
20 label=${ str($label).replace(",","-") }, 20 label=${ str($label).replace(",","-") },
21 #end if 21 #end if
22 #if $groups: 22 #if $groups:
23 groups=${ str($groups).replace(",","-") }, 23 groups=${ str($groups).replace(",","-") },
24 #end if 24 #end if
25 #if $sets: 25 #if $sets:
26 sets=${ str($sets).replace(",","-") }, 26 sets=${ str($sets).replace(",","-") },
27 #end if 27 #end if
28 iters=$iters, 28 iters=$iters,
29 threshold=$threshold, 29 threshold=$threshold,
30 processors='\${GALAXY_SLOTS:-8}' 30 processors='\${GALAXY_SLOTS:-8}'
31 )' 31 )'
32 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 33 | mothur
34 | tee mothur.out.log 34 | tee mothur.out.log
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 37 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
38 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> 38 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
39 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
49 <filter type="data_meta" ref="otu" key="groups"/> 49 <filter type="data_meta" ref="otu" key="groups"/>
50 </options> 50 </options>
51 </param> 51 </param>
52 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/> 52 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/>
53 <param name="threshold" type="float" value="0.05" min="0" max="1" label="threshold - significance level to reject null hypotheses"/> 53 <param name="threshold" type="float" value="0.05" min="0" max="1" label="threshold - significance level to reject null hypotheses"/>
54 <expand macro="param-savelog"/>
54 </inputs> 55 </inputs>
55 <outputs> 56 <outputs>
56 <expand macro="logfile-output"/> 57 <expand macro="logfile-output"/>
57 <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats"> 58 <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats">
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/> 59 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/>
61 <tests> 62 <tests>
62 <test> 63 <test>
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 64 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
64 <param name="design" value="toymothur.design2" ftype="mothur.design"/> 65 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
65 <output_collection name="metastats" count="36"> 66 <output_collection name="metastats" count="36">
66 <element name="0.23.tardis-dalek" ftype="txt"> 67 <element name="0.23.tardis_dalek" ftype="txt">
67 <assert_contents> 68 <assert_contents>
68 <has_text text="group1"/> 69 <has_text text="group1"/>
69 <has_text text="group2"/> 70 <has_text text="group2"/>
70 <has_text text="OTU"/> 71 <has_text text="OTU"/>
71 <has_text text="variance"/> 72 <has_text text="variance"/>
72 <has_text text="1000 permutations"/> 73 <has_text text="1000 permutations"/>
73 </assert_contents> 74 </assert_contents>
74 </element> 75 </element>
75 </output_collection> 76 </output_collection>
77 <param name="savelog" value="true"/>
76 <expand macro="logfile-test"/> 78 <expand macro="logfile-test"/>
77 </test> 79 </test>
78 <test> 80 <test>
79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 81 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
80 <param name="design" value="toymothur.design2" ftype="mothur.design"/> 82 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
82 <param name="threshold" value="0.1"/> 84 <param name="threshold" value="0.1"/>
83 <param name="label" value="0.03,0.05,0.23"/> 85 <param name="label" value="0.03,0.05,0.23"/>
84 <param name="groups" value="forest,pasture"/> 86 <param name="groups" value="forest,pasture"/>
85 <param name="sets" value="tardis,dalek"/> 87 <param name="sets" value="tardis,dalek"/>
86 <output_collection name="metastats" count="3"> 88 <output_collection name="metastats" count="3">
87 <element name="0.23.tardis-dalek" ftype="txt"> 89 <element name="0.23.tardis_dalek" ftype="txt">
88 <assert_contents> 90 <assert_contents>
89 <has_text text="group1"/> 91 <has_text text="group1"/>
90 <has_text text="group2"/> 92 <has_text text="group2"/>
91 <has_text text="OTU"/> 93 <has_text text="OTU"/>
92 <has_text text="variance"/> 94 <has_text text="variance"/>
93 <has_text text="42 permutations"/> 95 <has_text text="42 permutations"/>
94 </assert_contents> 96 </assert_contents>
95 </element> 97 </element>
96 </output_collection> 98 </output_collection>
99 <param name="savelog" value="true"/>
97 <expand macro="logfile-test"/> 100 <expand macro="logfile-test"/>
98 </test> 101 </test>
99 </tests> 102 </tests>
100 <help> 103 <help><![CDATA[
101 <![CDATA[
102 104
103 @MOTHUR_OVERVIEW@ 105 @MOTHUR_OVERVIEW@
104 106
105 **Command Documentation** 107 **Command Documentation**
106 108
107 The metastats_ command generate principle components plot data. 109 The metastats_ command generate principle components plot data.
108 110
109 .. _metastats: https://www.mothur.org/wiki/Metastats 111 .. _metastats: https://www.mothur.org/wiki/Metastats
110 112
111 v.1.21.0: Updated to mothur 1.33 113 v.1.21.0: Updated to mothur 1.33
112 ]]> 114
113 </help> 115 ]]></help>
114 <expand macro="citations"/> 116 <expand macro="citations"/>
115 </tool> 117 </tool>