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comparison core_diversity_analyses.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_core_diversity" name="Compute core set of diversity analyses" version="1.9.1">
2 <description></description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <version_command><![CDATA[
11 core_diversity_analyses.py --version
12 ]]>
13 </version_command>
14
15 <command>
16 <![CDATA[
17 core_diversity_analyses.py
18 -i $input_biom_fp
19 -o core_diversity_analyses
20 -m $mapping_fp
21 -e $sampling_depth
22
23 #if $parameter_fp
24 -p $parameter_fp
25 #end if
26
27 $parallel
28 -O "\${GALAXY_SLOTS:-4}"
29
30 #if $phylogenetic.nonphylogenetic_diversity
31 --nonphylogenetic_diversity
32 #else
33 -t $phylogenetic.tree_fp
34 #end if
35
36 $suppress_taxa_summary
37 $suppress_beta_diversity
38 $suppress_alpha_diversity
39 $suppress_group_significance
40
41 #if $categories
42 -c $categories
43 #end if
44
45 &&
46 mkdir -p $html_report.files_path
47 &&
48 cp -r core_diversity_analyses/* $html_report.files_path
49 &&
50 mv $html_report.files_path/index.html $html_report
51 ]]>
52 </command>
53
54 <inputs>
55 <param name="input_biom_fp" type="data" format="tabular,txt,tsv,biom"
56 label="OTU table" help="(-i/--input_biom_fp)"/>
57
58 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
59 label="Mapping file" help="(-m/--mapping_fp)"/>
60
61 <param name="sampling_depth" type="integer" value="" label="Sequencing
62 depth to use for even sub-sampling and maximum rarefaction depth"
63 help="To decide this value, review the output of the
64 ‘biom summarize-table’ (-e/--sampling_depth)"/>
65
66 <param name="parameter_fp" type="data" format="txt"
67 label="Parameter file" help="It specifies changes to the default
68 behavior (-p/--parameter_fp)" optional="true"/>
69
70 <param name="parallel" type="boolean" label="Run in parallel where
71 available?" truevalue="--parallel" falsevalue="" checked="true"
72 help="(-a, --parallel)" />
73
74 <conditional name="phylogenetic">
75 <param name="nonphylogenetic_diversity" type="boolean" label="Apply
76 non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis)
77 diversity calculations?" truevalue="--nonphylogenetic_diversity"
78 falsevalue="" checked="false" help="This is useful if, for example,
79 when working with non-amplicon BIOM tables, or if a reliable tree
80 is not available (--nonphylogenetic_diversity)" />
81 <when value="false" >
82 <param name="tree_fp" type="data" format="txt"
83 label="Tree file" help="(-t/--tree_fp)"/>
84 </when>
85 <when value="true" />
86 </conditional>
87
88 <param name="suppress_taxa_summary" type="boolean" label="Suppress
89 generation of taxa summary plots?" truevalue="--suppress_taxa_summary"
90 falsevalue="" checked="False" help="(--suppress_taxa_summary)" />
91
92 <param name="suppress_beta_diversity" type="boolean" label="Suppress
93 beta diversity analyses?" truevalue="--suppress_beta_diversity"
94 falsevalue="" checked="False" help="(--suppress_beta_diversity)" />
95
96 <param name="suppress_alpha_diversity" type="boolean" label="Suppress
97 alpha diversity analyses?" truevalue="--suppress_alpha_diversity"
98 falsevalue="" checked="False" help="(--suppress_alpha_diversity)" />
99
100 <param name="suppress_group_significance" type="boolean" label="Suppress
101 OTU/category significance analysis?" truevalue="--suppress_group_significance"
102 falsevalue="" checked="False" help="(--suppress_group_significance)" />
103
104 <param name="categories" type="text" value="" label="Metadata category or
105 categories to compare for categorical analyses (optional)"
106 help="The column headers in the mapping file should be passed as a
107 comma-separated list. By default, no categorical analyses are performed
108 (-c/--categories)" optional="true"/>
109
110 </inputs>
111
112 <outputs>
113 <data name="html_report" format="html"
114 label="${tool.name} on ${on_string}: Core diversity report" />
115 </outputs>
116
117 <tests>
118 <test>
119 </test>
120 </tests>
121
122 <help><![CDATA[
123
124 **What it does?**
125
126 This tool calculates alpha diversity, or within-sample diversity, using an
127 OTU table.
128
129 The resulting file(s) is a tab-delimited text file, where the columns correspond
130 to alpha diversity metrics and the rows correspond to samples and their calculated
131 diversity measurements. When a folder is given as input (-i), the script processes
132 every otu table file in the given folder, and creates a corresponding file in the
133 output directory.
134
135 More information about this tool is available on
136 `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
137 ]]>
138 </help>
139
140 <citations>
141 <expand macro="citations" />
142 </citations>
143 </tool>