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comparison mantel.xml @ 2:c9352db87f4c 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 22:18:20 -0400
parents 04aa7542e2df
children 17b471efdc40
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1:f6befaf69818 2:c9352db87f4c
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 "$dist2" dist2.dat && 14 ln -s '$dist2' dist2.dat &&
15 15
16 echo 'mantel( 16 echo 'mantel(
17 phylip1=dist.dat, 17 phylip1=dist.dat,
18 phylip2=dist2.dat, 18 phylip2=dist2.dat,
19 method=$method, 19 method=$method,
20 iters=$iters 20 iters=$iters
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 name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
28 <param name="dist2" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/> 28 <param name="dist2" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/>
29 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson"> 29 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
30 <option value="pearson" selected="true">pearson</option> 30 <option value="pearson" selected="true">pearson</option>
31 <option value="spearman">spearman</option> 31 <option value="spearman">spearman</option>
32 <option value="kendall">kendall</option> 32 <option value="kendall">kendall</option>
33 </param> 33 </param>
34 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> 34 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
35 <expand macro="param-savelog"/>
35 </inputs> 36 </inputs>
36 <outputs> 37 <outputs>
37 <expand macro="logfile-output"/> 38 <expand macro="logfile-output"/>
38 <data name="mantel" format="tabular" from_work_dir="dist*.mantel" label="${tool.name} on ${on_string}: mantel"/> 39 <data name="mantel" format="tabular" from_work_dir="dist*.mantel" label="${tool.name} on ${on_string}: mantel"/>
39 </outputs> 40 </outputs>
44 <output name="mantel" ftype="tabular"> 45 <output name="mantel" ftype="tabular">
45 <assert_contents> 46 <assert_contents>
46 <has_line_matching expression="^Mantel\tpValue$"/> 47 <has_line_matching expression="^Mantel\tpValue$"/>
47 </assert_contents> 48 </assert_contents>
48 </output> 49 </output>
50 <param name="savelog" value="true"/>
49 <expand macro="logfile-test"/> 51 <expand macro="logfile-test"/>
50 </test> 52 </test>
51 </tests> 53 </tests>
52 <help> 54 <help><![CDATA[
53 <![CDATA[
54 55
55 @MOTHUR_OVERVIEW@ 56 @MOTHUR_OVERVIEW@
56 57
57 **Command Documentation** 58 **Command Documentation**
58 59
59 The mantel_ command calculates the Mantel correlation coefficient between two matrices_. 60 The mantel_ command calculates the Mantel correlation coefficient between two matrices_.
60 61
61 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix 62 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
62 .. _mantel: https://www.mothur.org/wiki/Mantel 63 .. _mantel: https://www.mothur.org/wiki/Mantel
63 64
64 ]]> 65 ]]></help>
65 </help>
66 <expand macro="citations"/> 66 <expand macro="citations"/>
67 </tool> 67 </tool>