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comparison mantel.xml @ 0:04aa7542e2df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:32:35 -0400
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1 <tool profile="16.07" id="mothur_mantel" name="Mantel" version="@WRAPPER_VERSION@.0">
2 <description>Mantel correlation coefficient between two matrices.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat &&
14 ln -s "$dist2" dist2.dat &&
15
16 echo 'mantel(
17 phylip1=dist.dat,
18 phylip2=dist2.dat,
19 method=$method,
20 iters=$iters
21 )'
22 | sed 's/ //g' ## mothur trips over whitespace
23 | mothur
24 | tee mothur.out.log
25 ]]></command>
26 <inputs>
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"/>
29 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
30 <option value="pearson" selected="true">pearson</option>
31 <option value="spearman">spearman</option>
32 <option value="kendall">kendall</option>
33 </param>
34 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
35 </inputs>
36 <outputs>
37 <expand macro="logfile-output"/>
38 <data name="mantel" format="tabular" from_work_dir="dist*.mantel" label="${tool.name} on ${on_string}: mantel"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="dist" value="veg.dist"/>
43 <param name="dist2" value="env.dist"/>
44 <output name="mantel" ftype="tabular">
45 <assert_contents>
46 <has_line_matching expression="^Mantel\tpValue$"/>
47 </assert_contents>
48 </output>
49 <expand macro="logfile-test"/>
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 @MOTHUR_OVERVIEW@
56
57 **Command Documentation**
58
59 The mantel_ command calculates the Mantel correlation coefficient between two matrices_.
60
61 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
62 .. _mantel: https://www.mothur.org/wiki/Mantel
63
64 ]]>
65 </help>
66 <expand macro="citations"/>
67 </tool>