Mercurial > repos > iuc > mothur_corr_axes
comparison corr.axes.xml @ 0:9961b707d075 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 06:00:46 -0400 |
parents | |
children | 4e4035bf57df |
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-1:000000000000 | 0:9961b707d075 |
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1 <tool profile="16.07" id="mothur_corr_axes" name="Corr.axes" version="@WRAPPER_VERSION@.0"> | |
2 <description>correlation of data to axes</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <expand macro="version_command"/> | |
9 | |
10 <command><![CDATA[ | |
11 @SHELL_OPTIONS@ | |
12 | |
13 ## create symlinks to input datasets | |
14 #if $input.source == "shared": | |
15 ln -s "$input.otu" input.otu.dat && | |
16 #else | |
17 ln -s "$input.metadata" input.metadata.dat && | |
18 #end if | |
19 | |
20 echo 'corr.axes( | |
21 #if $input.source == "shared": | |
22 #if $input.otu.is_of_type("mothur.relabund"): | |
23 relabund=input.otu.dat, | |
24 #elif $input.otu.is_of_type("mothur.shared"): | |
25 shared=input.otu.dat, | |
26 #end if | |
27 #if $input.label: | |
28 label=$input.label, | |
29 #end if | |
30 #if $input.groups: | |
31 groups=${ str($input.groups).replace(",","-") }, | |
32 #end if | |
33 #else: | |
34 metadata=input.metadata.dat, | |
35 #end if | |
36 method=$method, | |
37 axes=$axes, | |
38 numaxes=$numaxes | |
39 )' | |
40 | sed 's/ //g' ## mothur trips over whitespace | |
41 | mothur | |
42 | tee mothur.out.log | |
43 ]]></command> | |
44 <inputs> | |
45 <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/> | |
46 <conditional name="input"> | |
47 <param name="source" type="select" label="Generate Collector Curvers for"> | |
48 <option value="shared">OTU Shared or Relabund</option> | |
49 <option value="metadata">Metadata table</option> | |
50 </param> | |
51 <when value="shared"> | |
52 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/> | |
53 <param name="label" type="select" label="label - OTU Labels" multiple="false" optional="true"> | |
54 <expand macro="labeloptions"/> | |
55 </param> | |
56 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> | |
57 <options> | |
58 <filter type="data_meta" ref="otu" key="groups"/> | |
59 </options> | |
60 </param> | |
61 </when> | |
62 <when value="metadata"> | |
63 <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values" help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/> | |
64 </when> | |
65 </conditional> | |
66 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson"> | |
67 <option value="pearson" selected="true">pearson</option> | |
68 <option value="spearman">spearman</option> | |
69 <option value="kendall">kendall</option> | |
70 </param> | |
71 <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/> | |
72 </inputs> | |
73 <outputs> | |
74 <expand macro="logfile-output"/> | |
75 <data name="corr_axes" format="mothur.axes" from_work_dir="input.*.axes" label="${tool.name} on ${on_string}: corr.axes"/> | |
76 </outputs> | |
77 <tests> | |
78 <test><!-- test with shared file --> | |
79 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/> | |
80 <param name="source" value="shared"/> | |
81 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | |
82 <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/> | |
83 <expand macro="logfile-test"/> | |
84 </test> | |
85 <test><!-- test with metadata file --> | |
86 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/> | |
87 <param name="source" value="metadata"/> | |
88 <param name="metadata" value="amazon.metadata" ftype="tabular"/> | |
89 <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/> | |
90 <expand macro="logfile-test"/> | |
91 </test> | |
92 <test><!-- test with relabund file and label and group select --> | |
93 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/> | |
94 <param name="source" value="shared"/> | |
95 <param name="label" value="0.05"/> | |
96 <param name="groups" value="forest,pasture"/> | |
97 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> | |
98 <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/> | |
99 <expand macro="logfile-test"/> | |
100 </test> | |
101 </tests> | |
102 <help> | |
103 <![CDATA[ | |
104 | |
105 @MOTHUR_OVERVIEW@ | |
106 | |
107 **Command Documentation** | |
108 | |
109 The corr.axes_ command calculates the correlation of data to axes. | |
110 | |
111 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes | |
112 | |
113 v.1.21.0: Updated to mothur 1.33 | |
114 | |
115 ]]> | |
116 </help> | |
117 <expand macro="citations"/> | |
118 </tool> |