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comparison beta_diversity_through_plots.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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-1:000000000000 0:c1bd0c560018
1 <tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance
2 matrices" version="1.9.1">
3
4 <description>and generate PCoA plots</description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <version_command><![CDATA[
13 beta_diversity_through_plots.py --version
14 ]]>
15 </version_command>
16
17 <stdio>
18 <regex match="VisibleDeprecationWarning"
19 source="both"
20 level="warning"
21 description="VisibleDeprecationWarning on numpy for `rank`" />
22 </stdio>
23
24 <command>
25 <![CDATA[
26 beta_diversity_through_plots.py
27 -i $otu_table_fp
28 -m $mapping_fp
29 -o beta_diversity_through_plots
30
31 #if $tree_fp
32 -t $tree_fp
33 #end if
34
35 #if $parameter_fp
36 -p $parameter_fp
37 #end if
38
39 $parallel
40 -O "\${GALAXY_SLOTS:-4}"
41
42 #if $seqs_per_sample
43 -e $seqs_per_sample
44 #end if
45
46 $suppress_emperor_plots
47
48 &&
49
50 python $__tool_directory__/beta_diversity_through_plots_html_generation.py
51 --data_directory beta_diversity_through_plots
52 --html_file $beta_diversity_pcoa
53 --html_dir $beta_diversity_pcoa.files_path
54
55 ]]>
56 </command>
57
58 <inputs>
59 <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom"
60 label="OTU table" help="(-i/--otu_table_fp)"
61 multiple="True"/>
62
63 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
64 label="Mapping file" help="(-m/--mapping_fp)"
65 multiple="True"/>
66
67 <param name="tree_fp" type="data" format="txt"
68 label="Tree file (Optional)" help="(-t/--tree_fp)"
69 optional="True"/>
70
71 <param name="parameter_fp" type="data" format="txt"
72 label="Parameter file (Optional)" help="It specifies changes to the default
73 behavior, e.g. beta diversity metrics (-p/--parameter_fp)"
74 optional="true"/>
75
76 <param name="color_by_all_fields" type="text" label="Colored mapping
77 fields" optional="True" help="Can be included only fields with
78 greater than one value and fewer values than the number of samples
79 (--color_by_all_fields)" />
80
81 <param name="parallel" type="boolean" label="Run in parallel where
82 available?" truevalue="--parallel" falsevalue="" checked="False"
83 help="(-a, --parallel)" />
84
85 <param name="seqs_per_sample" type="integer" label="Depth of coverage for
86 even sampling (Optional)" help="(-e/--seqs_per_sample)" optional="True"/>
87
88 <param name="suppress_emperor_plots" type="boolean" label="Generate
89 emperor plots?" truevalue="" falsevalue="--suppress_emperor_plots" checked="True"
90 help="(--suppress_emperor_plots)" />
91
92 </inputs>
93
94 <outputs>
95 <data format="txt" name="beta_diversity_matrix">
96 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt"
97 directory="beta_diversity_through_plots" visible="true" />
98 </data>
99
100 <data format="txt" name="beta_diversity_pc">
101 <discover_datasets pattern="(?P&lt;designation&gt;.+)_pc\.txt" ext="txt"
102 directory="beta_diversity_through_plots" visible="true" />
103 </data>
104
105 <data format="html" name="beta_diversity_pcoa"
106 label="${tool.name} on ${on_string}: PCoA"/>
107 </outputs>
108
109 <tests>
110 <test>
111 </test>
112 </tests>
113
114 <help><![CDATA[
115 **What it does**
116
117 This tool computes beta diversity distance matrices and generates PCoA plots in
118 several steps
119
120 - Performs beta diversity analysis
121 - Performs principal coordinate analysis
122 - Generates 3D PCoA Plots
123
124 More information about this tool is available on
125 `QIIME documentation <http://qiime.org/scripts/beta_diversity_through_plots.html>`_.
126 ]]>
127 </help>
128
129 <citations>
130 <expand macro="citations" />
131 </citations>
132 </tool>