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comparison rarefaction.shared.xml @ 2:7c3d6982fcef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:10:03 -0400
parents f17cc7d2fa71
children 419266a5e29e
comparison
equal deleted inserted replaced
1:ac51f9ce6160 2:7c3d6982fcef
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 #if $designc.usedesign == "yes": 14 #if $designc.usedesign == "yes":
15 ln -s "$designc.design" designc.design.dat && 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(",","-") },
16 #end if 30 #end if
17 31 #end if
18 echo 'rarefaction.shared( 32 #if $subsample.usess == "yes":
19 shared=otu.dat, 33 #if $subsample.subsamplesize:
20 #if $label: 34 subsample=$subsample.subsamplesize,
21 label=${ str($label).replace(",","-") }, 35 #else
22 #end if 36 subsample=T,
23 #if $groups 37 #end if
24 groups=${ str($groups).replace(",","-") }, 38 #if $subsample.subsampleiters:
25 #end if 39 subsampleiters=$subsample.subsampleiters,
26 #if $designc.usedesign == "yes": 40 #end if
27 design=designc.design.dat, 41 #end if
28 #if $designc.sets: 42 calc=${ str($calc).replace(",","-") },
29 sets=${ str($designc.sets).replace(",","-") }, 43 iters=$iters
30 #end if 44 $jumble
31 #end if 45 )'
32 #if $subsample.usess == "yes": 46 | sed 's/ //g' ## mothur trips over whitespace
33 #if $subsample.subsamplesize: 47 | mothur
34 subsample=$subsample.subsamplesize, 48 | tee mothur.out.log
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> 49 ]]></command>
50 <inputs> 50 <inputs>
51 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 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"> 52 <param name="label" type="select" label="label - OTU Labels" multiple="true">
53 <expand macro="labeloptions"/> 53 <expand macro="labeloptions"/>
54 </param> 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"> 55 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"
56 help="All groups will be analyzed by default if none are selected">
56 <options> 57 <options>
57 <filter type="data_meta" ref="otu" key="groups"/> 58 <filter type="data_meta" ref="otu" key="groups"/>
58 </options> 59 </options>
59 </param> 60 </param>
60 <conditional name="designc"> 61 <conditional name="designc">
61 <param name="usedesign" type="select" label="run on a per set basis using a design file?"> 62 <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="no" selected="true">no</option>
63 <option value="yes">yes</option> 64 <option value="yes">yes</option>
64 </param> 65 </param>
65 <when value="yes"> 66 <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="design" type="data" format="mothur.design" label="design - assigns groups to sets"
68 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"> 69 <param name="sets" type="select" multiple="true" label="sets - group sets to analyze">
68 <options> 70 <options>
69 <filter type="data_meta" ref="design" key="groups"/> 71 <filter type="data_meta" ref="design" key="groups"/>
70 </options> 72 </options>
71 </param> 73 </param>
72 </when> 74 </when>
73 <when value="no"/> 75 <when value="no"/>
74 </conditional> 76 </conditional>
75 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/> 77 <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"/> 78 <param name="jumble" type="boolean" truevalue=",jumble=true" falsevalue="" checked="false" label="jumble?"
79 help="Obviously, the goal of rarefaction is to randomize across the samples; however, if you just want a
80 collector's curve across the samples you can use the jumble option"/>
77 <param name="calc" type="select" label="calc - Calculators " multiple="true"> 81 <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> 82 <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> 83 <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
80 </param> 84 </param>
81 <conditional name="subsample"> 85 <conditional name="subsample">
82 <param name="usess" type="select" label="produce subsample rarefactions?"> 86 <param name="usess" type="select" label="produce subsample rarefactions?">
83 <option value="no" selected="true">no</option> 87 <option value="no" selected="true">no</option>
84 <option value="yes">yes</option> 88 <option value="yes">yes</option>
85 </param> 89 </param>
86 <when value="yes"> 90 <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"/> 91 <param name="subsamplesize" type="integer" value="" optional="true" label="subsample - size pergroup of the sample"
92 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"/> 93 <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/>
89 </when> 94 </when>
90 <when value="no"/> 95 <when value="no"/>
91 </conditional> 96 </conditional>
97 <expand macro="param-savelog"/>
92 </inputs> 98 </inputs>
93 <outputs> 99 <outputs>
94 <expand macro="logfile-output"/> 100 <expand macro="logfile-output"/>
95 <data name="rarefaction" format="tabular" from_work_dir="otu.shared.rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction"> 101 <data name="rarefaction" format="tabular" from_work_dir="otu.shared.rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction">
96 <filter>designc['usedesign'] == 'no' and 'sharedobserved' in calc</filter> 102 <filter>designc['usedesign'] == 'no' and 'sharedobserved' in calc</filter>
122 <has_text text="0.22"/> 128 <has_text text="0.22"/>
123 <has_text text="0.33"/> 129 <has_text text="0.33"/>
124 <has_text text="0.55"/> 130 <has_text text="0.55"/>
125 </assert_contents> 131 </assert_contents>
126 </output> 132 </output>
133 <param name="savelog" value="true"/>
127 <expand macro="logfile-test"/> 134 <expand macro="logfile-test"/>
128 </test> 135 </test>
129 <test><!-- test with label, group and calc select --> 136 <test><!-- test with label, group and calc select -->
130 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 137 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
131 <param name="groups" value="forest,pasture"/> 138 <param name="groups" value="forest,pasture"/>
151 <has_text text="0.22"/> 158 <has_text text="0.22"/>
152 <not_has_text text="0.33"/> 159 <not_has_text text="0.33"/>
153 <has_text text="0.55"/> 160 <has_text text="0.55"/>
154 </assert_contents> 161 </assert_contents>
155 </output> 162 </output>
163 <param name="savelog" value="true"/>
156 <expand macro="logfile-test"/> 164 <expand macro="logfile-test"/>
157 </test> 165 </test>
158 <test><!-- test with design file --> 166 <test><!-- test with design file -->
159 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 167 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
160 <param name="usedesign" value="yes"/> 168 <param name="usedesign" value="yes"/>
169 <has_text text="0.22"/> 177 <has_text text="0.22"/>
170 <has_text text="0.33"/> 178 <has_text text="0.33"/>
171 <has_text text="0.55"/> 179 <has_text text="0.55"/>
172 </assert_contents> 180 </assert_contents>
173 </output> 181 </output>
182 <param name="savelog" value="true"/>
174 <expand macro="logfile-test"/> 183 <expand macro="logfile-test"/>
175 </test> 184 </test>
176 <test><!-- test with subsampling --> 185 <!-- segfaults when subsampling on some files, known bug, devs promise to fix in next release
177 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 186 <test><!- - test with subsampling - ->
187 <param name="otu" value="esophagus.fn.shared" ftype="mothur.shared"/>
178 <param name="usess" value="yes"/> 188 <param name="usess" value="yes"/>
179 <param name="subsamplesize" value="10"/>
180 <param name="subsampleiters" value="42"/> 189 <param name="subsampleiters" value="42"/>
181 <param name="calc" value="sharedobserved,sharednseqs"/> 190 <param name="calc" value="sharedobserved,sharednseqs"/>
182 <output name="rarefaction"> 191 <output name="rarefaction">
183 <assert_contents> 192 <assert_contents>
184 <has_text text="numsampled"/> 193 <has_text text="numsampled"/>
212 <has_text text="std"/> 221 <has_text text="std"/>
213 <has_text text="0.14"/> 222 <has_text text="0.14"/>
214 </assert_contents> 223 </assert_contents>
215 </element> 224 </element>
216 </output_collection> 225 </output_collection>
217 <expand macro="logfile-test"/> 226 <param name="savelog" value="true"/>
218 </test> 227 <expand macro="logfile-test"/>
228 </test>-->
219 </tests> 229 </tests>
220 <help> 230 <help><![CDATA[
221 <![CDATA[
222 231
223 @MOTHUR_OVERVIEW@ 232 @MOTHUR_OVERVIEW@
224 233
225 **Command Documentation** 234 **Command Documentation**
226 235
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 236 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
228 237
229 .. _rarefaction.shared: https://www.mothur.org/wiki/Rarefaction.shared 238 .. _rarefaction.shared: https://www.mothur.org/wiki/Rarefaction.shared
230 ]]> 239
231 </help> 240 ]]></help>
232 <expand macro="citations"/> 241 <expand macro="citations"/>
233 </tool> 242 </tool>