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comparison homova.xml @ 2:2ccbfa78b831 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 21:58:39 -0400
parents d891666964ad
children 68005ede9e6e
comparison
equal deleted inserted replaced
1:d4c1caf95426 2:2ccbfa78b831
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 "$dist" dist.dat && 13 ln -s '$dist' dist.dat &&
14 ln -s "$design" design.dat && 14 ln -s '$design' design.dat &&
15 15
16 echo 'homova( 16 echo 'homova(
17 phylip=dist.dat, 17 phylip=dist.dat,
18 design=design.dat, 18 design=design.dat,
19 #if $sets: 19 #if $sets:
20 sets=${ str($sets).replace(",","-") }, 20 sets=${ str($sets).replace(",","-") },
21 #end if 21 #end if
22 iters=$iters, 22 iters=$iters,
23 alpha=$alpha 23 alpha=$alpha
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 name="dist" 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 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> 31 <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)"/>
32 <param name="alpha" type="float" optional="true" value="0.05" min="0.0" label="alpha - acceptable stopping precision (default 0.05)"/> 32 <param name="alpha" type="float" optional="true" value="0.05" min="0.0" label="alpha - acceptable stopping precision (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. The set names are separated by dashes. The default is all sets in designfile"> 34 <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in designfile">
35 <options> 35 <options>
36 <filter type="data_meta" ref="design" key="groups"/> 36 <filter type="data_meta" ref="design" key="groups"/>
37 </options> 37 </options>
38 </param> 38 </param>
39 <expand macro="param-savelog"/>
39 </inputs> 40 </inputs>
40 <outputs> 41 <outputs>
41 <expand macro="logfile-output"/> 42 <expand macro="logfile-output"/>
42 <data name="homova" format="tabular" from_work_dir="dist*.homova" label="${tool.name} on ${on_string}: homova"/> 43 <data name="homova" format="tabular" from_work_dir="dist*.homova" label="${tool.name} on ${on_string}: homova"/>
43 </outputs> 44 </outputs>
49 <assert_contents> 50 <assert_contents>
50 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/> 51 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
51 <has_text text="A-B"/> 52 <has_text text="A-B"/>
52 </assert_contents> 53 </assert_contents>
53 </output> 54 </output>
55 <param name="savelog" value="true"/>
54 <expand macro="logfile-test"/> 56 <expand macro="logfile-test"/>
55 </test> 57 </test>
56 <test><!-- test with subsets --> 58 <test><!-- test with subsets -->
57 <param name="dist" value="amazon.dist" ftype="mothur.dist"/> 59 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
58 <param name="design" value="amazon.design" ftype="mothur.design"/> 60 <param name="design" value="amazon.design" ftype="mothur.design"/>
61 <assert_contents> 63 <assert_contents>
62 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/> 64 <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
63 <has_line_matching expression="A\t.*$"/> 65 <has_line_matching expression="A\t.*$"/>
64 </assert_contents> 66 </assert_contents>
65 </output> 67 </output>
68 <param name="savelog" value="true"/>
66 <expand macro="logfile-test"/> 69 <expand macro="logfile-test"/>
67 </test> 70 </test>
68 </tests> 71 </tests>
69 <help> 72 <help><![CDATA[
70 <![CDATA[
71 73
72 @MOTHUR_OVERVIEW@ 74 @MOTHUR_OVERVIEW@
73 75
74 **Command Documentation** 76 **Command Documentation**
75 77
88 90
89 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 91 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
90 .. _homova: https://www.mothur.org/wiki/Homova 92 .. _homova: https://www.mothur.org/wiki/Homova
91 93
92 v.1.20.0: Updated to Mothur 1.33, added sets parameter 94 v.1.20.0: Updated to Mothur 1.33, added sets parameter
93 ]]> 95
94 </help> 96 ]]></help>
95 <expand macro="citations"/> 97 <expand macro="citations"/>
96 </tool> 98 </tool>