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comparison jackknifed_beta_diversity.xml @ 0:f9df45b8425a 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 09:31:46 -0400
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children 205f4c9739c0
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1 <tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0">
2 <description>and building jackknifed PCoA plots</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <stdio>
8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
9 <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/>
10 </stdio>
11 <version_command>jackknifed_beta_diversity.py --version</version_command>
12 <command detect_errors="aggressive"><![CDATA[
13 jackknifed_beta_diversity.py
14 --otu_table_fp '$otu_table_fp'
15 --mapping_fp '$mapping_fp'
16 -o jackknifed_beta_diversity
17 --seqs_per_sample '$seqs_per_sample'
18 #if $tree_fp
19 --tree_fp '$tree_fp'
20 #end if
21 #if $parameter_fp
22 --parameter_fp '$parameter_fp'
23 #end if
24 --master_tree '$master_tree'
25 $parallel
26 -O "\${GALAXY_SLOTS:-4}"
27
28 && python $__tool_directory__/jackknifed_beta_diversity_output_management.py
29 --data_directory jackknifed_beta_diversity
30 --html_file '$jackknifed_beta_diversity_report'
31 --html_dir '$jackknifed_beta_diversity_report.files_path'
32 ]]></command>
33 <inputs>
34 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/>
35 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/>
36 <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/>
37 <param argument="--tree_fp" type="data" format="txt" label="Tree file" help="It is required for phylogenetic measures" optional="True"/>
38 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
39 <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis">
40 <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
41 <option value="full">Tree generated from input (unsubsambled) otu table</option>
42 </param>
43 <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>
44 </inputs>
45 <outputs>
46 <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity">
47 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>
48 </collection>
49 <collection name="unrarefied_beta_div_tree" type="list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity">
50 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tre" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>
51 </collection>
52 <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">
53 <discover_datasets pattern="rarefaction_(?P&lt;designation&gt;.+)\.biom" directory="jackknifed_beta_diversity/rarefaction/"/>
54 </collection>
55 <collection name="pcoa" type="list:list" label="${tool.name} on ${on_string}: PCoA">
56 <discover_datasets pattern="pcoa_(?P&lt;identifier_0&gt;.+)_rarefaction_(?P&lt;identifier_1&gt;.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/pcoa/"/>
57 </collection>
58 <collection name="rare_dm" type="list:list" label="${tool.name} on ${on_string}: Distance matrix for rarefied beta diversity">
59 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_rarefaction_(?P&lt;identifier_1&gt;.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/rare_dm/"/>
60 </collection>
61 <collection name="rare_upgma" type="list:list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity">
62 <discover_datasets pattern="upgma_(?P&lt;identifier_0&gt;.+)_rarefaction_(?P&lt;identifier_1&gt;.+)\.tre" ext="txt" directory="jackknifed_beta_diversity/rare_upgma/"/>
63 </collection>
64 <collection name="rare_upgma_consensus" type="list" label="${tool.name} on ${on_string}: Consensus UPGMA trees for unrarefied beta diversity">
65 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tre" directory="jackknifed_beta_diversity/rare_upgma_consensus/"/>
66 </collection>
67 <data name="jackknifed_beta_diversity_report" format="html" label="${tool.name} on ${on_string}: Report"/>
68 </outputs>
69 <tests>
70 <test>
71 <param name="otu_table_fp" value="jackknifed_beta_diversity/otu_table.biom"/>
72 <param name="mapping_fp" value="jackknifed_beta_diversity/map.txt"/>
73 <param name="seqs_per_sample" value="10"/>
74 <param name="tree_fp" value="jackknifed_beta_diversity/rep_set.tre"/>
75 <param name="master_tree" value="consensus"/>
76 <param name="parallel" value="--parallel"/>
77 <output_collection name="unrarefied_beta_div_dist_matrix" type="list" count="2"/>
78 <output_collection name="unrarefied_beta_div_tree" type="list" count="2"/>
79 <output_collection name="rarefaction" type="list" count="10"/>
80 <output_collection name="pcoa" type="list:list">
81 <element name="unweighted_unifrac">
82 <element name="10_0">
83 <assert_contents>
84 <has_text text="PC.636" />
85 <has_text text="PC.635" />
86 <has_text text="PC.356" />
87 <has_text text="PC.481" />
88 <has_text text="PC.354" />
89 <has_text text="PC.593" />
90 <has_text text="PC.355" />
91 <has_text text="PC.607" />
92 <has_text text="PC.634" />
93 </assert_contents>
94 </element>
95 </element>
96 <element name="weighted_unifrac">
97 <element name="10_0">
98 <assert_contents>
99 <has_text text="PC.636" />
100 <has_text text="PC.635" />
101 <has_text text="PC.356" />
102 <has_text text="PC.481" />
103 <has_text text="PC.354" />
104 <has_text text="PC.593" />
105 <has_text text="PC.355" />
106 <has_text text="PC.607" />
107 <has_text text="PC.634" />
108 </assert_contents>
109 </element>
110 </element>
111 </output_collection>
112 <output_collection name="rare_dm" type="list:list">
113 <element name="unweighted_unifrac">
114 <element name="10_0">
115 <assert_contents>
116 <has_text text="PC.636" />
117 <has_text text="PC.635" />
118 <has_text text="PC.356" />
119 <has_text text="PC.481" />
120 <has_text text="PC.354" />
121 <has_text text="PC.593" />
122 <has_text text="PC.355" />
123 <has_text text="PC.607" />
124 <has_text text="PC.634" />
125 </assert_contents>
126 </element>
127 </element>
128 <element name="weighted_unifrac">
129 <element name="10_0">
130 <assert_contents>
131 <has_text text="PC.636" />
132 <has_text text="PC.635" />
133 <has_text text="PC.356" />
134 <has_text text="PC.481" />
135 <has_text text="PC.354" />
136 <has_text text="PC.593" />
137 <has_text text="PC.355" />
138 <has_text text="PC.607" />
139 <has_text text="PC.634" />
140 </assert_contents>
141 </element>
142 </element>
143 </output_collection>
144 <output_collection name="rare_upgma" type="list:list">
145 <element name="unweighted_unifrac">
146 <element name="10_0">
147 <assert_contents>
148 <has_text text="PC.636" />
149 <has_text text="PC.635" />
150 <has_text text="PC.356" />
151 <has_text text="PC.481" />
152 <has_text text="PC.354" />
153 <has_text text="PC.593" />
154 <has_text text="PC.355" />
155 <has_text text="PC.607" />
156 <has_text text="PC.634" />
157 </assert_contents>
158 </element>
159 </element>
160 <element name="weighted_unifrac">
161 <element name="10_0">
162 <assert_contents>
163 <has_text text="PC.636" />
164 <has_text text="PC.635" />
165 <has_text text="PC.356" />
166 <has_text text="PC.481" />
167 <has_text text="PC.354" />
168 <has_text text="PC.593" />
169 <has_text text="PC.355" />
170 <has_text text="PC.607" />
171 <has_text text="PC.634" />
172 </assert_contents>
173 </element>
174 </element>
175 </output_collection>
176 <output_collection name="rare_upgma_consensus" type="list" count="2">
177 <element name="unweighted_unifrac">
178 <assert_contents>
179 <has_text text="PC.636" />
180 <has_text text="PC.635" />
181 <has_text text="PC.356" />
182 <has_text text="PC.481" />
183 <has_text text="PC.354" />
184 <has_text text="PC.593" />
185 <has_text text="PC.355" />
186 <has_text text="PC.607" />
187 <has_text text="PC.634" />
188 </assert_contents>
189 </element>
190 <element name="weighted_unifrac">
191 <assert_contents>
192 <has_text text="PC.636" />
193 <has_text text="PC.635" />
194 <has_text text="PC.356" />
195 <has_text text="PC.481" />
196 <has_text text="PC.354" />
197 <has_text text="PC.593" />
198 <has_text text="PC.355" />
199 <has_text text="PC.607" />
200 <has_text text="PC.634" />
201 </assert_contents>
202 </element>
203 </output_collection>
204 <output name="jackknifed_beta_diversity_report">
205 <assert_contents>
206 <has_text text="unweighted_unifrac" />
207 <has_text text="weighted_unifrac" />
208 </assert_contents>
209 </output>
210 </test>
211 </tests>
212 <help><![CDATA[
213 **What it does**
214
215 This tool performs jackknifing (repeatedly resampling a subset of the available data from each sample) to measure robustness of individual UPGMA clusters and clusters in PCoA plots.
216
217 More information about this tool is available on
218 `QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_.
219 ]]></help>
220 <citations>
221 <expand macro="citations"/>
222 </citations>
223 </tool>