Mercurial > repos > iuc > mothur_otu_hierarchy
view otu.hierarchy.xml @ 4:abf3d41b7428 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author | iuc |
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date | Mon, 23 Apr 2018 09:56:18 -0400 |
parents | 058e6e36f6e5 |
children | 2e82b56377d8 |
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<tool profile="16.07" id="mothur_otu_hierarchy" name="Otu.hierarchy" version="@WRAPPER_VERSION@.0"> <description>Relate OTUs at different distances</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$otu' otu.dat && echo 'otu.hierarchy( list=otu.dat, label=$label1-$label2, output=$output )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> <param name="label1" type="select" label="label - OTU Label 1"> <expand macro="labeloptions"/> </param> <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1"> <expand macro="labeloptions"/> </param> <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers"> <option value="name" selected="true">OTU sequence names</option> <option value="number">OTU numbers</option> </param> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> </outputs> <tests> <test> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="label1" value="0.05"/> <param name="label2" value="0.03"/> <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The otu.hierarchy_ command relates OTUs from a list_ at different distances. .. _list: https://www.mothur.org/wiki/List_file .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy ]]></help> <expand macro="citations"/> </tool>