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comparison core_diversity_analyses.xml @ 0:2a7e18c4a657 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:37:30 -0400
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children 61e86fd975a4
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-1:000000000000 0:2a7e18c4a657
1 <tool id="qiime_core_diversity" name="Compute core set of diversity analyses" version="@WRAPPER_VERSION@.0">
2 <description>A workflow for running a core set of QIIME diversity analyses</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>core_diversity_analyses.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 ## set matplotlib backend
10 echo "backend:agg" > matplotlibrc &&
11
12 core_diversity_analyses.py
13 --input_biom_fp '$input_biom_fp'
14 -o core_diversity_analyses
15 --mapping_fp '$mapping_fp'
16 --sampling_depth '$sampling_depth'
17 #if $parameter_fp
18 --parameter_fp '$parameter_fp'
19 #end if
20 $parallel
21 -O "\${GALAXY_SLOTS:-4}"
22 $phylogenetic.nonphylogenetic_diversity
23 #if str( $phylogenetic.nonphylogenetic_diversity ) == ""
24 --tree_fp '$phylogenetic.tree_fp'
25 #end if
26 $suppress_taxa_summary
27 $suppress_beta_diversity
28 $suppress_alpha_diversity
29 $suppress_group_significance
30 #if str( $categories ):
31 --categories '$categories'
32 #end if
33
34 && mkdir -p '$html_report.files_path'
35 && cp -r core_diversity_analyses/* '$html_report.files_path'
36 && mv '$html_report.files_path/index.html' '$html_report'
37 ]]></command>
38 <inputs>
39 <param argument="--input_biom_fp" type="data" format="tabular,txt,biom,h5" label="OTU table"/>
40 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" />
41 <param argument="--sampling_depth" type="integer" value="" label="Sequencing depth to use for even sub-sampling and maximum rarefaction depth" help="To decide this value, review the output of the ‘biom summarize-table’"/>
42 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior" optional="true"/>
43 <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>
44 <conditional name="phylogenetic">
45 <param argument="--nonphylogenetic_diversity" type="select" label="Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations?" help="This is useful if, for example, when working with non-amplicon BIOM tables, or if a reliable tree is not available">
46 <option value="--nonphylogenetic_diversity">Yes</option>
47 <option value="" selected="true">No</option>
48 </param>
49 <when value="">
50 <param argument="--tree_fp" type="data" format="txt" label="Tree file"/>
51 </when>
52 <when value="--nonphylogenetic_diversity"/>
53 </conditional>
54 <param argument="--suppress_taxa_summary" type="boolean" label="Suppress generation of taxa summary plots?" truevalue="--suppress_taxa_summary" falsevalue="" checked="False"/>
55 <param argument="--suppress_beta_diversity" type="boolean" label="Suppress beta diversity analyses?" truevalue="--suppress_beta_diversity" falsevalue="" checked="False"/>
56 <param argument="--suppress_alpha_diversity" type="boolean" label="Suppress alpha diversity analyses?" truevalue="--suppress_alpha_diversity" falsevalue="" checked="False"/>
57 <param argument="--suppress_group_significance" type="boolean" label="Suppress OTU/category significance analysis?" truevalue="--suppress_group_significance" falsevalue="" checked="False"/>
58 <param argument="--categories" type="text" value="" label="Metadata category or categories to compare for categorical analyses (optional)" help="The column headers in the mapping file should be passed as a comma-separated list. By default, no categorical analyses are performed" optional="true"/>
59 </inputs>
60 <outputs>
61 <data name="html_report" format="html" label="${tool.name} on ${on_string}: Core diversity report"/>
62 </outputs>
63 <tests>
64 <test> <!-- test taxa summary and group significance -->
65 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
66 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
67 <param name="sampling_depth" value="22"/>
68 <param name="parallel" value="--parallel"/>
69 <param name="nonphylogenetic_diversity" value=""/>
70 <param name="tree_fp" value="core_diversity_analyses/rep_set.tre"/>
71 <param name="suppress_taxa_summary" value=""/>
72 <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
73 <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
74 <param name="suppress_group_significance" value=""/>
75 <output name="html_report">
76 <assert_contents>
77 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
78 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
79 <has_text text="Taxa summary bar plots"/>
80 </assert_contents>
81 </output>
82 </test>
83 <test><!-- test beta diversity -->
84 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
85 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
86 <param name="sampling_depth" value="22"/>
87 <param name="parallel" value="--parallel"/>
88 <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
89 <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
90 <param name="suppress_beta_diversity" value=""/>
91 <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
92 <param name="suppress_group_significance" value="--suppress_group_significance"/>
93 <output name="html_report">
94 <assert_contents>
95 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
96 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
97 <has_text text="Beta diversity results"/>
98 </assert_contents>
99 </output>
100 </test>
101 <test><!-- test suppressing all -->
102 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
103 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
104 <param name="sampling_depth" value="22"/>
105 <param name="parallel" value="--parallel"/>
106 <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
107 <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
108 <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
109 <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
110 <param name="suppress_group_significance" value="--suppress_group_significance"/>
111 <output name="html_report">
112 <assert_contents>
113 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
114 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
115 </assert_contents>
116 </output>
117 </test>
118 </tests>
119 <help><![CDATA[
120 **What it does**
121
122 This tool calculates alpha diversity, or within-sample diversity, using an
123 OTU table.
124
125 The resulting file(s) is a tab-delimited text file, where the columns correspond
126 to alpha diversity metrics and the rows correspond to samples and their calculated
127 diversity measurements. When a folder is given as input (-i), the script processes
128 every otu table file in the given folder, and creates a corresponding file in the
129 output directory.
130
131 More information about this tool is available on
132 `QIIME documentation <http://qiime.org/scripts/core_diversity_analyses.html>`_.
133 ]]></help>
134 <citations>
135 <expand macro="citations"/>
136 </citations>
137 </tool>