Mercurial > repos > iuc > mothur_normalize_shared
view normalize.shared.xml @ 3:41da04156611 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author | iuc |
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date | Fri, 06 Apr 2018 04:08:33 -0400 |
parents | 0493525c9b4f |
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<tool profile="16.07" id="mothur_normalize_shared" name="Normalize.shared" version="@WRAPPER_VERSION@.0"> <description>Normalize the number of sequences per group to a specified level</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 'normalize.shared( #if $otu.is_of_type("mothur.relabund"): relabund=otu.dat #elif $otu.is_of_type("mothur.shared"): shared=otu.dat, makerelabund=$makerelabund #end if #if $label: ,label=${ str($label).replace(",","-") } #end if #if $groups: ,groups=${ str($groups).replace(",","-") } #end if #if $method: ,method=${ str($method).replace(",","-") } #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> <param name="label" type="select" multiple="true" label="label - OTU Labels"> <expand macro="labeloptions"/> </param> <param name="groups" type="select" multiple="true" label="groups - Groups to include"> <options> <filter type="data_meta" ref="otu" key="groups"/> </options> </param> <param name="method" type="select" label="method - Normalization method"> <option value="totalgroup" selected="true">Total Group</option> <option value="zscore">Z Score</option> </param> <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection"> <discover_datasets pattern=".*?\.(?P<designation>.*)\.shared" format="mothur.shared"/> </collection> </outputs> <tests> <test><!-- test default settings --> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <output_collection name="sharedfiles" count="36"> <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test default settings --> <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> <param name="label" value="0.03,0.05,0.22,0.26"/> <param name="groups" value="forest,pasture"/> <param name="method" value="zscore"/> <output_collection name="sharedfiles" count="4"> <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file. .. _shared: https://www.mothur.org/wiki/Shared_file .. _relabund: https://www.mothur.org/wiki/Get.relabund .. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared ]]></help> <expand macro="citations"/> </tool>