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comparison amova.xml @ 2:fcb95815087f 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 22:16:06 -0400
parents 0d34975c52a0
children 5aa5d26efeea
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1:65b7b1a17c1c 2:fcb95815087f
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 "$dist" dist.dat && 13 ln -s '$phylip' phylip.dat &&
14 ln -s "$design" design.dat && 14 ln -s '$design' design.dat &&
15 15
16 echo 'amova( 16 echo 'amova(
17 phylip=dist.dat, 17 phylip=phylip.dat,
18 iters=$iters, 18 iters=$iters,
19 alpha=$alpha, 19 alpha=$alpha,
20 #if $sets: 20 #if $sets:
21 sets=$sets, 21 sets=${ str($sets).replace(",","-") },
22 #end if 22 #end if
23 design=design.dat 23 design=design.dat
24 )' 24 )'
25 | sed 's/ //g' ## mothur trips over whitespace 25 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur 26 | mothur
27 | tee mothur.out.log 27 | tee mothur.out.log
28 ]]></command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 30 <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
31 <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)"/> 31 <param argument="design" type="data" format="mothur.design" label="design - assign groups to new grouping"
32 <param name="alpha" type="float" optional="true" min="0" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> 32 help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)"/>
33 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/> 33 <param argument="alpha" type="float" optional="true" min="0" value="0.05" label="alpha - acceptable stopping precision" help="default: 0.05"/>
34 <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze." help="The set names are separated by dashes. The defualt is all sets in designfile"> 34 <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/>
35 <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
36 <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
37 <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
38 help="The set names are separated by dashes. The defualt is all sets in designfile">
35 <options> 39 <options>
36 <filter type="data_meta" ref="design" key="sets"/> 40 <filter type="data_meta" ref="design" key="sets"/>
37 </options> 41 </options>
38 </param> 42 </param>
43 -->
44 <expand macro="param-savelog"/>
39 </inputs> 45 </inputs>
40 <outputs> 46 <outputs>
41 <expand macro="logfile-output"/> 47 <expand macro="logfile-output"/>
42 <data name="amova" format="tabular" from_work_dir="dist.amova" label="${tool.name} on ${on_string}: amova"/> 48 <data name="amova" format="tabular" from_work_dir="phylip.amova" label="${tool.name} on ${on_string}: amova"/>
43 </outputs> 49 </outputs>
44 <tests> 50 <tests>
45 <test> 51 <test>
46 <param name="dist" value="amazon.dist"/> 52 <param name="phylip" value="amazon.dist"/>
47 <param name="design" value="amazon.design"/> 53 <param name="design" value="amazon.design"/>
48 <output name="amova" ftype="tabular"> 54 <output name="amova" ftype="tabular">
49 <assert_contents> 55 <assert_contents>
50 <has_line_matching expression="^A-B\tAmong\tWithin\tTotal$"/> 56 <has_line_matching expression="^A-B\tAmong\tWithin\tTotal$"/>
51 <has_line_matching expression="^SS\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/> 57 <has_line_matching expression="^SS\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
52 <has_line_matching expression="^df\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/> 58 <has_line_matching expression="^df\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
53 <has_line_matching expression="^MS\t[0-9\.]+\t[0-9\.]+$"/> 59 <has_line_matching expression="^MS\t[0-9\.]+\t[0-9\.]+$"/>
54 <has_text text="p-value"/> 60 <has_text text="p-value"/>
55 </assert_contents> 61 </assert_contents>
56 </output> 62 </output>
63 <param name="savelog" value="true"/>
64 <expand macro="logfile-test"/>
65 </test>
66 <test><!-- test with sets specified -->
67 <param name="phylip" value="amazon.dist"/>
68 <param name="design" value="amazon.design"/>
69 <param name="sets" value="A,B"/>
70 <output name="amova" ftype="tabular">
71 <assert_contents>
72 <has_line_matching expression="^A-B\tAmong\tWithin\tTotal$"/>
73 <has_line_matching expression="^SS\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
74 <has_line_matching expression="^df\t[0-9\.]+\t[0-9\.]+\t[0-9\.]+$"/>
75 <has_line_matching expression="^MS\t[0-9\.]+\t[0-9\.]+$"/>
76 <has_text text="p-value"/>
77 </assert_contents>
78 </output>
79 <param name="savelog" value="true"/>
57 <expand macro="logfile-test"/> 80 <expand macro="logfile-test"/>
58 </test> 81 </test>
59 </tests> 82 </tests>
60 <help> 83 <help><![CDATA[
61 <![CDATA[
62 84
63 @MOTHUR_OVERVIEW@ 85 @MOTHUR_OVERVIEW@
64 86
65 **Command Documentation** 87 **Command Documentation**
66 88
67 The amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations. 89 The amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_,
90 a nonparametric analog of traditional analysis of variance. This method is widely used in population
91 genetics to test the hypothesis that genetic diversity within two populations is not significantly
92 different from that which would result from pooling the two populations.
68 93
69 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : 94 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
70 ======= ======= 95 ======= =======
71 duck bird 96 duck bird
72 cow mammal 97 cow mammal
79 104
80 105
81 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 106 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
82 .. _amova: https://www.mothur.org/wiki/Amova 107 .. _amova: https://www.mothur.org/wiki/Amova
83 108
84 ]]> 109 ]]></help>
85 </help>
86 <expand macro="citations"/> 110 <expand macro="citations"/>
87 </tool> 111 </tool>