Mercurial > repos > iuc > mothur_anosim

comparison anosim.xml @ 2:d83e7e498f31 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 22:09:48 -0400
parents 08ccc12f2a3a
children 652d2803062c
comparison
equal deleted inserted replaced
1:f228c52a3978 2:d83e7e498f31
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 'anosim( 16 echo 'anosim(
17 phylip=dist.dat, 17 phylip=phylip.dat,
18 iters=$iters, 18 iters=$iters,
19 alpha=$alpha, 19 alpha=$alpha,
20 design=design.dat 20 design=design.dat
21 )' 21 )'
22 | sed 's/ //g' ## mothur trips over whitespace 22 | sed 's/ //g' ## mothur trips over whitespace
23 | mothur 23 | mothur
24 | tee mothur.out.log 24 | tee mothur.out.log
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 27 <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
28 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> 28 <param argument="design" type="data" format="tabular" label="design - assign groups to new grouping"
29 <param name="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision (default 0.05)"/> 29 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
30 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/> 30 <param argument="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision" help="default: 0.05"/>
31 <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/>
32 <expand macro="param-savelog"/>
31 </inputs> 33 </inputs>
32 <outputs> 34 <outputs>
33 <expand macro="logfile-output"/> 35 <expand macro="logfile-output"/>
34 <data name="anosim" format="tabular" from_work_dir="dist.anosim" label="${tool.name} on ${on_string}: anosim"/> 36 <data name="anosim" format="tabular" from_work_dir="phylip.anosim" label="${tool.name} on ${on_string}: anosim"/>
35 </outputs> 37 </outputs>
36 <tests> 38 <tests>
37 <test> 39 <test>
38 <param name="dist" value="amazon.dist"/> 40 <param name="phylip" value="amazon.dist"/>
39 <param name="design" value="amazon.design"/> 41 <param name="design" value="amazon.design"/>
40 <output name="anosim" ftype="tabular"> 42 <output name="anosim" ftype="tabular">
41 <assert_contents> 43 <assert_contents>
42 <has_line_matching expression="^comparison\tR-value\tP-value$"/> 44 <has_line_matching expression="^comparison\tR-value\tP-value$"/>
43 <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/> 45 <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/>
44 </assert_contents> 46 </assert_contents>
45 </output> 47 </output>
48 <param name="savelog" value="true"/>
46 <expand macro="logfile-test"/> 49 <expand macro="logfile-test"/>
47 </test> 50 </test>
48 </tests> 51 </tests>
49 <help> 52 <help><![CDATA[
50 <![CDATA[
51 53
52 @MOTHUR_OVERVIEW@ 54 @MOTHUR_OVERVIEW@
53 55
54 **Command Documentation** 56 **Command Documentation**
55 57
68 70
69 71
70 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 72 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
71 .. _anosim: https://www.mothur.org/wiki/Anosim 73 .. _anosim: https://www.mothur.org/wiki/Anosim
72 74
73 ]]> 75 ]]></help>
74 </help>
75 <expand macro="citations"/> 76 <expand macro="citations"/>
76 </tool> 77 </tool>