Mercurial > repos > iuc > mothur_corr_axes

comparison corr.axes.xml @ 2:4e4035bf57df draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:08:33 -0400
parents 9961b707d075
children 0968daa9b52f
comparison
equal deleted inserted replaced
1:456cf87a12a6 2:4e4035bf57df
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 9
10 <command><![CDATA[ 10 <command><![CDATA[
11 @SHELL_OPTIONS@ 11 @SHELL_OPTIONS@
12 12
13 ## create symlinks to input datasets 13 ## create symlinks to input datasets
14 #if $input.source == "shared": 14 #if $input.source == "shared":
15 ln -s "$input.otu" input.otu.dat && 15 ln -s '$input.otu' input.otu.dat &&
16 #else 16 #else
17 ln -s "$input.metadata" input.metadata.dat && 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,
18 #end if 26 #end if
19 27 #if $input.label:
20 echo 'corr.axes( 28 label=$input.label,
21 #if $input.source == "shared": 29 #end if
22 #if $input.otu.is_of_type("mothur.relabund"): 30 #if $input.groups:
23 relabund=input.otu.dat, 31 groups=${ str($input.groups).replace(",","-") },
24 #elif $input.otu.is_of_type("mothur.shared"): 32 #end if
25 shared=input.otu.dat, 33 #else:
26 #end if 34 metadata=input.metadata.dat,
27 #if $input.label: 35 #end if
28 label=$input.label, 36 method=$method,
29 #end if 37 axes=$axes,
30 #if $input.groups: 38 numaxes=$numaxes
31 groups=${ str($input.groups).replace(",","-") }, 39 )'
32 #end if 40 | sed 's/ //g' ## mothur trips over whitespace
33 #else: 41 | mothur
34 metadata=input.metadata.dat, 42 | tee mothur.out.log
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> 43 ]]></command>
44 <inputs> 44 <inputs>
45 <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/> 45 <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/>
46 <conditional name="input"> 46 <conditional name="input">
47 <param name="source" type="select" label="Generate Collector Curvers for"> 47 <param name="source" type="select" label="Generate Collector Curvers for">
58 <filter type="data_meta" ref="otu" key="groups"/> 58 <filter type="data_meta" ref="otu" key="groups"/>
59 </options> 59 </options>
60 </param> 60 </param>
61 </when> 61 </when>
62 <when value="metadata"> 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.)"/> 63 <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values"
64 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 </when>
65 </conditional> 66 </conditional>
66 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson"> 67 <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="pearson" selected="true">pearson</option>
68 <option value="spearman">spearman</option> 69 <option value="spearman">spearman</option>
69 <option value="kendall">kendall</option> 70 <option value="kendall">kendall</option>
70 </param> 71 </param>
71 <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/> 72 <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/>
73 <expand macro="param-savelog"/>
72 </inputs> 74 </inputs>
73 <outputs> 75 <outputs>
74 <expand macro="logfile-output"/> 76 <expand macro="logfile-output"/>
75 <data name="corr_axes" format="mothur.axes" from_work_dir="input.*.axes" label="${tool.name} on ${on_string}: corr.axes"/> 77 <data name="corr_axes" format="mothur.axes" from_work_dir="input.*.axes" label="${tool.name} on ${on_string}: corr.axes"/>
76 </outputs> 78 </outputs>
78 <test><!-- test with shared file --> 80 <test><!-- test with shared file -->
79 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/> 81 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
80 <param name="source" value="shared"/> 82 <param name="source" value="shared"/>
81 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 83 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
82 <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/> 84 <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/>
85 <param name="savelog" value="true"/>
83 <expand macro="logfile-test"/> 86 <expand macro="logfile-test"/>
84 </test> 87 </test>
85 <test><!-- test with metadata file --> 88 <test><!-- test with metadata file -->
86 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/> 89 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
87 <param name="source" value="metadata"/> 90 <param name="source" value="metadata"/>
88 <param name="metadata" value="amazon.metadata" ftype="tabular"/> 91 <param name="metadata" value="amazon.metadata" ftype="tabular"/>
89 <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/> 92 <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/>
93 <param name="savelog" value="true"/>
90 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
91 </test> 95 </test>
92 <test><!-- test with relabund file and label and group select --> 96 <test><!-- test with relabund file and label and group select -->
93 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/> 97 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
94 <param name="source" value="shared"/> 98 <param name="source" value="shared"/>
95 <param name="label" value="0.05"/> 99 <param name="label" value="0.05"/>
96 <param name="groups" value="forest,pasture"/> 100 <param name="groups" value="forest,pasture"/>
97 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> 101 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
98 <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/> 102 <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/>
103 <param name="savelog" value="true"/>
99 <expand macro="logfile-test"/> 104 <expand macro="logfile-test"/>
100 </test> 105 </test>
101 </tests> 106 </tests>
102 <help> 107 <help><![CDATA[
103 <![CDATA[
104 108
105 @MOTHUR_OVERVIEW@ 109 @MOTHUR_OVERVIEW@
106 110
107 **Command Documentation** 111 **Command Documentation**
108 112
110 114
111 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes 115 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
112 116
113 v.1.21.0: Updated to mothur 1.33 117 v.1.21.0: Updated to mothur 1.33
114 118
115 ]]> 119 ]]></help>
116 </help>
117 <expand macro="citations"/> 120 <expand macro="citations"/>
118 </tool> 121 </tool>