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comparison alpha_rarefaction.xml @ 0:a92964d8290f 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 09:19:14 -0400
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children 32f9caa12a80
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-1:000000000000 0:a92964d8290f
1 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0">
2 <description>A workflow script for performing alpha rarefaction</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>alpha_rarefaction.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 ## set matplotlib backend
10 echo "backend:agg" > matplotlibrc &&
11
12 alpha_rarefaction.py
13 --otu_table_fp '$otu_table_fp'
14 --mapping_fp '$mapping_fp'
15 -o alpha_rarefaction
16 #if $parameter_fp
17 --parameter_fp '$parameter_fp'
18 #end if
19 --num_steps '$num_steps'
20 $parallel
21 -O "\${GALAXY_SLOTS:-4}"
22 #if $tree_fp
23 --tree_fp '$tree_fp'
24 #end if
25 --min_rare_depth '$min_rare_depth'
26 #if $max_rare_depth
27 --max_rare_depth '$max_rare_depth'
28 #end if
29 $retain_intermediate_files
30
31 && mkdir -p $alpha_rarefaction_plots.files_path
32 && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
33 && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
34 ]]></command>
35 <inputs>
36 <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/>
37 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/>
38 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
39 <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/>
40 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/>
41 <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="True" label="Tree file (optional)" help="Required for phylogenetic measures"/>
42 <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/>
43 <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/>
44 <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="True" label="Retain intermediate files?"/>
45 </inputs>
46 <outputs>
47 <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
48 <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information">
49 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/>
50 </collection>
51 <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">
52 <discover_datasets pattern="rarefaction_(?P&lt;designation&gt;.+)\.biom" directory="alpha_rarefaction/rarefaction/"/>
53 <filter>retain_intermediate_files!=''</filter>
54 </collection>
55 <collection name="alpha_div" type="list" label="${tool.name} on ${on_string}: Alpha diversity results">
56 <discover_datasets pattern="alpha_rarefaction_(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div/"/>
57 <filter>retain_intermediate_files!=''</filter>
58 </collection>
59 </outputs>
60 <tests>
61 <test>
62 <param name="otu_table_fp" value="alpha_rarefaction/otu_table.biom"/>
63 <param name="mapping_fp" value="alpha_rarefaction/mapping_file.txt"/>
64 <param name="num_steps" value="2"/>
65 <param name="parallel" value=""/>
66 <param name="tree_fp" value="alpha_rarefaction/rep_set.tre"/>
67 <param name="min_rare_depth" value="10"/>
68 <param name="max_rare_depth" value="50"/>
69 <param name="retain_intermediate_files" value="--retain_intermediate_files"/>
70 <output name="alpha_rarefaction_plots">
71 <assert_contents>
72 <has_text text="Control_mouse_I.D._354" />
73 </assert_contents>
74 </output>
75 <output_collection name="alpha_diversity" type="list" count="3">
76 <element name="chao1">
77 <assert_contents>
78 <has_text text="alpha_rarefaction_10_0" />
79 <has_text text="alpha_rarefaction_30_5" />
80 <has_text text="alpha_rarefaction_50_9" />
81 </assert_contents>
82 </element>
83 <element name="observed_otus">
84 <assert_contents>
85 <has_text text="alpha_rarefaction_10_0" />
86 <has_text text="alpha_rarefaction_30_5" />
87 <has_text text="alpha_rarefaction_50_9" />
88 </assert_contents>
89 </element>
90 <element name="PD_whole_tree">
91 <assert_contents>
92 <has_text text="alpha_rarefaction_10_0" />
93 <has_text text="alpha_rarefaction_30_5" />
94 <has_text text="alpha_rarefaction_50_9" />
95 </assert_contents>
96 </element>
97 </output_collection>
98 <output_collection name="rarefaction" type="list" count="30">
99 <element name="10_0">
100 <assert_contents>
101 <has_text text="PC.636" />
102 <has_text text="PC.354" />
103 <has_text text="PC.634" />
104 </assert_contents>
105 </element>
106 <element name="30_6">
107 <assert_contents>
108 <has_text text="PC.636" />
109 <has_text text="PC.354" />
110 <has_text text="PC.634" />
111 </assert_contents>
112 </element>
113 <element name="50_9">
114 <assert_contents>
115 <has_text text="PC.636" />
116 <has_text text="PC.354" />
117 <has_text text="PC.634" />
118 </assert_contents>
119 </element>
120 </output_collection>
121 <output_collection name="alpha_div" type="list" count="30">
122 <element name="10_0">
123 <assert_contents>
124 <has_text text="PC.636" />
125 <has_text text="PC.354" />
126 <has_text text="PC.634" />
127 </assert_contents>
128 </element>
129 <element name="30_6">
130 <assert_contents>
131 <has_text text="PC.636" />
132 <has_text text="PC.354" />
133 <has_text text="PC.634" />
134 </assert_contents>
135 </element>
136 <element name="50_9">
137 <assert_contents>
138 <has_text text="PC.636" />
139 <has_text text="PC.354" />
140 <has_text text="PC.634" />
141 </assert_contents>
142 </element>
143 </output_collection>
144 </test>
145 </tests>
146 <help><![CDATA[
147 **What it does**
148
149 This script performs alpha rarefaction in several steps:
150
151 - Generation of rarefied OTU tables
152 - Computation of alpha diversity metrics for each rarefied OTU table
153 - Concatenation of alpha diversity results
154 - Generation of alpha rarefaction plots
155
156 More information about this tool is available on
157 `QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
158 ]]></help>
159 <citations>
160 <expand macro="citations"/>
161 </citations>
162 </tool>