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comparison pca.xml @ 0:52a9971dc4fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:44:22 -0400
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children 258d04c1c5f8
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-1:000000000000 0:52a9971dc4fa
1 <tool profile="16.07" id="mothur_pca" name="Pca" version="@WRAPPER_VERSION@.0">
2 <description>Principal Coordinate Analysis for a shared file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11
12 echo 'pca(
13 #if $otu.is_of_type("mothur.relabund"):
14 relabund=otu.dat,
15 #elif $otu.is_of_type("mothur.shared"):
16 shared=otu.dat,
17 #end if
18 #if $label:
19 label=${ str($label).replace(",","-") },
20 #end if
21 #if $groups:
22 groups=${ str($groups).replace(",","-") },
23 #end if
24 metric=$metric
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 ]]></command>
29 <inputs>
30 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
31 <param name="label" type="select" label="label - OTU Labels" multiple="true">
32 <expand macro="labeloptions"/>
33 </param>
34 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
35 <options>
36 <filter type="data_meta" ref="otu" key="groups"/>
37 </options>
38 </param>
39 <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
40 </inputs>
41 <outputs>
42 <expand macro="logfile-output"/>
43 <collection name="pca_axes" type="list" label="${tool.name} on ${on_string}: pca.axes">
44 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.axes" format="mothur.axes"/>
45 </collection>
46 <collection name="pca_loadings" type="list" label="${tool.name} on ${on_string}: pca.loadings">
47 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pca\.loadings" format="txt"/>
48 </collection>
49 </outputs>
50 <tests>
51 <test>
52 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
53 <param name="groups" value="forest,pasture"/>
54 <param name="label" value="0.22,0.55"/>
55 <output_collection name="pca_axes" count="2">
56 <element name="0.22" md5="4e32155fcfefe7d2f45b896d26b36409" ftype="mothur.axes"/>
57 </output_collection>
58 <output_collection name="pca_loadings" count="2">
59 <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/>
60 </output_collection>
61 <expand macro="logfile-test"/>
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66
67 @MOTHUR_OVERVIEW@
68
69 **Command Documenation**
70
71 The pca_ command generate principle components plot data for a shared_ or relabund_ file.
72
73 .. _shared: http://www.mothur.org/wiki/Shared_file
74 .. _relabund: http://www.mothur.org/wiki/Get.relabund
75 .. _pca: http://www.mothur.org/wiki/Pca
76 ]]>
77 </help>
78 <expand macro="citations"/>
79 </tool>