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comparison rarefaction.shared.xml @ 0:f17cc7d2fa71 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:24:46 -0400
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-1:000000000000 0:f17cc7d2fa71
1 <tool profile="16.07" id="mothur_rarefaction_shared" name="Rarefaction.shared" version="@WRAPPER_VERSION@.0">
2 <description>Generate inter-sample rarefaction curves for OTUs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14 #if $designc.usedesign == "yes":
15 ln -s "$designc.design" designc.design.dat &&
16 #end if
17
18 echo 'rarefaction.shared(
19 shared=otu.dat,
20 #if $label:
21 label=${ str($label).replace(",","-") },
22 #end if
23 #if $groups
24 groups=${ str($groups).replace(",","-") },
25 #end if
26 #if $designc.usedesign == "yes":
27 design=designc.design.dat,
28 #if $designc.sets:
29 sets=${ str($designc.sets).replace(",","-") },
30 #end if
31 #end if
32 #if $subsample.usess == "yes":
33 #if $subsample.subsamplesize:
34 subsample=$subsample.subsamplesize,
35 #else
36 subsample=T,
37 #end if
38 #if $subsample.subsampleiters:
39 subsampleiters=$subsample.subsampleiters,
40 #end if
41 #end if
42 calc=${ str($calc).replace(",","-") },
43 iters=$iters,
44 jumble=$jumble
45 )'
46 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur
48 | tee mothur.out.log
49 ]]></command>
50 <inputs>
51 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
52 <param name="label" type="select" label="label - OTU Labels" multiple="true">
53 <expand macro="labeloptions"/>
54 </param>
55 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true" help="All groups will be analyzed by default if none are selected">
56 <options>
57 <filter type="data_meta" ref="otu" key="groups"/>
58 </options>
59 </param>
60 <conditional name="designc">
61 <param name="usedesign" type="select" label="run on a per set basis using a design file?">
62 <option value="no" selected="true">no</option>
63 <option value="yes">yes</option>
64 </param>
65 <when value="yes">
66 <param name="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
67 <param name="sets" type="select" multiple="true" label="sets - group sets to analyze">
68 <options>
69 <filter type="data_meta" ref="design" key="groups"/>
70 </options>
71 </param>
72 </when>
73 <when value="no"/>
74 </conditional>
75 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/>
76 <param name="jumble" type="boolean" truevalue="true" falsevalue="false" checked="true" label="jumble"/>
77 <param name="calc" type="select" label="calc - Calculators " multiple="true">
78 <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
79 <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
80 </param>
81 <conditional name="subsample">
82 <param name="usess" type="select" label="produce subsample rarefactions?">
83 <option value="no" selected="true">no</option>
84 <option value="yes">yes</option>
85 </param>
86 <when value="yes">
87 <param name="subsamplesize" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" help="Leave blank to use the size of your smallest group"/>
88 <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/>
89 </when>
90 <when value="no"/>
91 </conditional>
92 </inputs>
93 <outputs>
94 <expand macro="logfile-output"/>
95 <data name="rarefaction" format="tabular" from_work_dir="otu.shared.rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction">
96 <filter>designc['usedesign'] == 'no' and 'sharedobserved' in calc</filter>
97 </data>
98 <data name="rarefaction2" format="tabular" from_work_dir="otu.shared.r_nseqs" label="${tool.name} on ${on_string}: shared.r_nseqs">
99 <filter>designc['usedesign'] == 'no' and 'sharednseqs' in calc</filter>
100 </data>
101 <data name="group_rarefaction" format="tabular" from_work_dir="otu.groups.rarefaction" label="${tool.name} on ${on_string}: groups.rarefaction">
102 <filter>designc['usedesign'] == 'yes'</filter>
103 </data>
104 <collection name="rarefaction_subsample_sharedobserved" type="list" label="${tool.name} on ${on_string}: shared.rarefaction">
105 <filter>subsample['usess'] == 'yes' and 'sharedobserved' in calc</filter>
106 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.rarefaction" format="tabular"/>
107 </collection>
108 <collection name="rarefaction_subsample_sharednseqs" type="list" label="${tool.name} on ${on_string}: shared.r_nseqs">
109 <filter>subsample['usess'] == 'yes' and 'sharednseqs' in calc</filter>
110 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.r_nseqs" format="tabular"/>
111 </collection>
112 </outputs>
113 <tests>
114 <test><!-- test with default values -->
115 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
116 <output name="rarefaction">
117 <assert_contents>
118 <has_text text="numsampled"/>
119 <has_text text="lci"/>
120 <has_text text="hci"/>
121 <has_text text="unique"/>
122 <has_text text="0.22"/>
123 <has_text text="0.33"/>
124 <has_text text="0.55"/>
125 </assert_contents>
126 </output>
127 <expand macro="logfile-test"/>
128 </test>
129 <test><!-- test with label, group and calc select -->
130 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
131 <param name="groups" value="forest,pasture"/>
132 <param name="label" value="0.22,0.55"/>
133 <param name="calc" value="sharedobserved,sharednseqs"/>
134 <output name="rarefaction">
135 <assert_contents>
136 <has_text text="numsampled"/>
137 <has_text text="lci"/>
138 <has_text text="hci"/>
139 <not_has_text text="unique"/>
140 <has_text text="0.22"/>
141 <not_has_text text="0.33"/>
142 <has_text text="0.55"/>
143 </assert_contents>
144 </output>
145 <output name="rarefaction2">
146 <assert_contents>
147 <has_text text="numsampled"/>
148 <has_text text="lci"/>
149 <has_text text="hci"/>
150 <not_has_text text="unique"/>
151 <has_text text="0.22"/>
152 <not_has_text text="0.33"/>
153 <has_text text="0.55"/>
154 </assert_contents>
155 </output>
156 <expand macro="logfile-test"/>
157 </test>
158 <test><!-- test with design file -->
159 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
160 <param name="usedesign" value="yes"/>
161 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
162 <param name="sets" value="tardis,dalek"/>
163 <output name="group_rarefaction">
164 <assert_contents>
165 <has_text text="numsampled"/>
166 <has_text text="lci"/>
167 <has_text text="hci"/>
168 <has_text text="unique"/>
169 <has_text text="0.22"/>
170 <has_text text="0.33"/>
171 <has_text text="0.55"/>
172 </assert_contents>
173 </output>
174 <expand macro="logfile-test"/>
175 </test>
176 <test><!-- test with subsampling -->
177 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
178 <param name="usess" value="yes"/>
179 <param name="subsamplesize" value="10"/>
180 <param name="subsampleiters" value="42"/>
181 <param name="calc" value="sharedobserved,sharednseqs"/>
182 <output name="rarefaction">
183 <assert_contents>
184 <has_text text="numsampled"/>
185 <has_text text="lci"/>
186 <has_text text="hci"/>
187 <has_text text="unique"/>
188 <has_text text="0.22"/>
189 <has_text text="0.33"/>
190 <has_text text="0.55"/>
191 </assert_contents>
192 </output>
193 <output_collection name="rarefaction_subsample_sharedobserved" count="36">
194 <element name="ave-std.0.14" ftype="tabular">
195 <assert_contents>
196 <has_text text="numsampled"/>
197 <has_text text="lci"/>
198 <has_text text="hci"/>
199 <has_text text="ave"/>
200 <has_text text="std"/>
201 <has_text text="0.14"/>
202 </assert_contents>
203 </element>
204 </output_collection>
205 <output_collection name="rarefaction_subsample_sharednseqs" count="36">
206 <element name="ave-std.0.14" ftype="tabular">
207 <assert_contents>
208 <has_text text="numsampled"/>
209 <has_text text="lci"/>
210 <has_text text="hci"/>
211 <has_text text="ave"/>
212 <has_text text="std"/>
213 <has_text text="0.14"/>
214 </assert_contents>
215 </element>
216 </output_collection>
217 <expand macro="logfile-test"/>
218 </test>
219 </tests>
220 <help>
221 <![CDATA[
222
223 @MOTHUR_OVERVIEW@
224
225 **Command Documentation**
226
227 The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
228
229 .. _rarefaction.shared: https://www.mothur.org/wiki/Rarefaction.shared
230 ]]>
231 </help>
232 <expand macro="citations"/>
233 </tool>