Mercurial > repos > iuc > mothur_summary_single

comparison summary.single.xml @ 8:88d39b1679df draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author iuc
date Thu, 05 Nov 2020 23:21:24 +0000
parents 3aeaa4ca1e48
children
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7:72be09dfd803 8:88d39b1679df
1 <tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.2">
2 <description>Summary of calculator values for OTUs</description> 2 <description>Summary of calculator values for OTUs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
48 )' 48 )'
49 | sed 's/ //g' ## mothur trips over whitespace 49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur 50 | mothur
51 | tee mothur.out.log 51 | tee mothur.out.log
52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode): 52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
53 && mv otu.*ave_std.summary otu.ave-std 53 && mv otu.*ave[_-]std.summary otu.ave-std
54 #end if 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">
113 <filter>otu.extension == 'mothur.shared' and not groupmode</filter> 113 <filter>otu.extension == 'mothur.shared' and not groupmode</filter>
114 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.summary" format="tabular"/> 114 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.summary" format="tabular"/>
115 </collection> 115 </collection>
116 </outputs> 116 </outputs>
117 <tests> 117 <tests>
118 <test><!-- test with shared and subsampling -->
119 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
120 <param name="use" value="yes"/>
121 <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
122 <param name="savelog" value="true"/>
123 <expand macro="logfile-test"/>
124 </test>
118 <test><!-- test with shared and default params --> 125 <test><!-- test with shared and default params -->
119 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 126 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
120 <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/> 127 <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
121 <param name="savelog" value="true"/> 128 <param name="savelog" value="true"/>
122 <expand macro="logfile-test"/> 129 <expand macro="logfile-test"/>