Mercurial > repos > iuc > mothur_anosim
view anosim.xml @ 2:d83e7e498f31 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:09:48 -0400 |
parents | 08ccc12f2a3a |
children | 652d2803062c |
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<tool profile="16.07" id="mothur_anosim" name="Anosim" version="@WRAPPER_VERSION@.0"> <description>Non-parametric multivariate analysis of changes in community structure</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 '$phylip' phylip.dat && ln -s '$design' design.dat && echo 'anosim( phylip=phylip.dat, iters=$iters, alpha=$alpha, design=design.dat )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> <param argument="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> <param argument="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision" help="default: 0.05"/> <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="anosim" format="tabular" from_work_dir="phylip.anosim" label="${tool.name} on ${on_string}: anosim"/> </outputs> <tests> <test> <param name="phylip" value="amazon.dist"/> <param name="design" value="amazon.design"/> <output name="anosim" ftype="tabular"> <assert_contents> <has_line_matching expression="^comparison\tR-value\tP-value$"/> <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure. A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : ======= ======= duck bird cow mammal pig mammal goose bird cobra reptile ======= ======= The Make_Design tool can construct a design file from a Mothur dataset that contains group names. .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _anosim: https://www.mothur.org/wiki/Anosim ]]></help> <expand macro="citations"/> </tool>