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comparison summary.single.xml @ 3:3aeaa4ca1e48 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 22:00:33 -0400
parents 9ea778acd657
children 88d39b1679df
comparison
equal deleted inserted replaced
2:3600fa8985ed 3:3aeaa4ca1e48
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 14
15 echo 'summary.single( 15 echo 'summary.single(
16 #if $otu.is_of_type("mothur.rabund"): 16 #if $otu.is_of_type("mothur.rabund"):
17 rabund=otu.dat 17 rabund=otu.dat
18 #elif $otu.is_of_type("mothur.sabund"): 18 #elif $otu.is_of_type("mothur.sabund"):
19 sabund=otu.dat 19 sabund=otu.dat
20 #elif $otu.is_of_type("mothur.list"): 20 #elif $otu.is_of_type("mothur.list"):
21 list=otu.dat 21 list=otu.dat
22 #elif $otu.is_of_type("mothur.shared"): 22 #elif $otu.is_of_type("mothur.shared"):
23 shared=otu.dat, 23 shared=otu.dat,
24 groupmode=$groupmode 24 groupmode=$groupmode
25 #end if 25 #end if
26 #if $label: 26 #if $label:
27 ,label=${ str($label).replace(",","-") } 27 ,label=${ str($label).replace(",","-") }
28 #end if 28 #end if
29 #if $calc: 29 #if $calc:
30 ,calc=${ str($calc).replace(",","-") } 30 ,calc=${ str($calc).replace(",","-") }
31 #end if 31 #end if
32 #if $abund: 32 #if $abund:
33 ,abund=$abund 33 ,abund=$abund
34 #end if 34 #end if
35 #if $size: 35 #if $size:
36 ,size=$size 36 ,size=$size
37 #end if 37 #end if
38 #if $subsample.use == 'yes': 38 #if $subsample.use == 'yes':
39 #if $subsample.subsample: 39 #if $subsample.subsample:
40 ,subsample=$subsample.subsample 40 ,subsample=$subsample.subsample
41 #else 41 #else
42 ,subsample=T 42 ,subsample=T
43 #end if
44 #if $subsample.iters:
45 ,iters=$subsample.iters
46 #end if
47 #end if
48 )'
49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur
51 | tee mothur.out.log
52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
53 && mv otu.*ave-std.summary otu.ave-std
54 #end if 43 #end if
44 #if $subsample.iters:
45 ,iters=$subsample.iters
46 #end if
47 #end if
48 )'
49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur
51 | tee mothur.out.log
52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
53 && mv otu.*ave_std.summary otu.ave-std
54 #end if
55 ]]></command> 55 ]]></command>
56 <inputs> 56 <inputs>
57 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> 57 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
58 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 58 <param name="label" type="select" label="label - OTU Labels" multiple="true">
59 <expand macro="labeloptions"/> 59 <expand macro="labeloptions"/>
97 <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/> 97 <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/>
98 </when> 98 </when>
99 <when value="no"/> 99 <when value="no"/>
100 </conditional> 100 </conditional>
101 <param name="groupmode" type="boolean" truevalue="true" falsevalue="false" checked="true" label="groupmode - Collate shared summary results in one file" help="If false, create a summary file per group."/> 101 <param name="groupmode" type="boolean" truevalue="true" falsevalue="false" checked="true" label="groupmode - Collate shared summary results in one file" help="If false, create a summary file per group."/>
102 <expand macro="param-savelog"/>
102 </inputs> 103 </inputs>
103 <outputs> 104 <outputs>
104 <expand macro="logfile-output"/> 105 <expand macro="logfile-output"/>
105 <data name="subsample_summary" format="tabular" from_work_dir="otu.ave-std" label="${tool.name} on ${on_string}: ave-std.summary"> 106 <data name="subsample_summary" format="tabular" from_work_dir="otu.ave-std" label="${tool.name} on ${on_string}: ave-std.summary">
106 <filter>subsample['use'] and not (otu.extension == 'mothur.shared' and not groupmode)</filter> 107 <filter>subsample['use'] and not (otu.extension == 'mothur.shared' and not groupmode)</filter>
115 </outputs> 116 </outputs>
116 <tests> 117 <tests>
117 <test><!-- test with shared and default params --> 118 <test><!-- test with shared and default params -->
118 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 119 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
119 <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/> 120 <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
121 <param name="savelog" value="true"/>
120 <expand macro="logfile-test"/> 122 <expand macro="logfile-test"/>
121 </test> 123 </test>
122 <test><!-- test with label select and all calculators --> 124 <test><!-- test with label select and all calculators -->
123 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 125 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
124 <param name="label" value="0.05,0.22,0.32"/> 126 <param name="label" value="0.05,0.22,0.32"/>
125 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/> 127 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/>
126 <output name="summary" md5="06039951e867e7d397db08aeb668f94f" ftype="tabular"/> 128 <output name="summary" md5="06039951e867e7d397db08aeb668f94f" ftype="tabular"/>
129 <param name="savelog" value="true"/>
127 <expand macro="logfile-test"/> 130 <expand macro="logfile-test"/>
128 </test> 131 </test>
129 <test><!-- test with shared and not groupmode --> 132 <test><!-- test with shared and not groupmode -->
130 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 133 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
131 <param name="groupmode" value="false"/> 134 <param name="groupmode" value="false"/>
132 <output_collection name="summaryfiles" count="2"> 135 <output_collection name="summaryfiles" count="2">
133 <element name="forest" md5="96e2c1213f25d6c342ba87ab3d2de6bf" ftype="tabular"/> 136 <element name="forest" md5="96e2c1213f25d6c342ba87ab3d2de6bf" ftype="tabular"/>
134 </output_collection> 137 </output_collection>
138 <param name="savelog" value="true"/>
135 <expand macro="logfile-test"/> 139 <expand macro="logfile-test"/>
136 </test> 140 </test>
137 <test><!-- test with rabund and subsample --> 141 <test><!-- test with rabund and subsample -->
138 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> 142 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
139 <param name="use" value="yes"/> 143 <param name="use" value="yes"/>
151 <has_text text="shannon"/> 155 <has_text text="shannon"/>
152 <has_text text="unique"/> 156 <has_text text="unique"/>
153 <has_text text="0.05"/> 157 <has_text text="0.05"/>
154 </assert_contents> 158 </assert_contents>
155 </output> 159 </output>
160 <param name="savelog" value="true"/>
156 <expand macro="logfile-test"/> 161 <expand macro="logfile-test"/>
157 </test> 162 </test>
158 </tests> 163 </tests>
159 <help> 164 <help><![CDATA[
160 <![CDATA[
161 165
162 @MOTHUR_OVERVIEW@ 166 @MOTHUR_OVERVIEW@
163 167
164 **Command Documentation** 168 **Command Documentation**
165 169
166 The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators 170 The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
167 171
168 .. _group: https://www.mothur.org/wiki/Group_file 172 .. _group: https://www.mothur.org/wiki/Group_file
169 .. _summary.single: https://www.mothur.org/wiki/Summary.single 173 .. _summary.single: https://www.mothur.org/wiki/Summary.single
170 ]]> 174
171 </help> 175 ]]></help>
172 <expand macro="citations"/> 176 <expand macro="citations"/>
173 </tool> 177 </tool>