Mercurial > repos > iuc > mothur_get_coremicrobiome
view get.coremicrobiome.xml @ 2:a1d38f9902d9 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 22:04:46 -0400 |
parents | fb34c63ab676 |
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<tool profile="16.07" id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="@WRAPPER_VERSION@.0"> <description>fraction of OTUs for samples or abundances</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 'get.coremicrobiome( #if $otu.is_of_type("mothur.relabund"): relabund=otu.dat #elif $otu.is_of_type("mothur.shared"): shared=otu.dat #end if #if $label: ,label=${ str($label).replace(",","-") } #end if #if $groups: ,groups=${ str($groups).replace(",","-") } #end if #if $abundance: ,abundance=$abundance #end if #if $samples: ,samples=$samples #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 or relabund - OTU Shared or Relabund"/> <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> <expand macro="labeloptions"/> </param> <param name="groups" type="select" optional="true" label="groups - Pairwise comparision groups" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups"/> </options> </param> <param name="abundance" type="integer" optional="true" value="" min="0" max="100" label="abundance - list OTU names at this abundance"/> <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/> <param name="output" type="select" label="output - fraction or count"> <option value="fraction" selected="true">fraction</option> <option value="count">count</option> </param> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files"> <discover_datasets pattern=".*?\.(?P<designation>.*)\.core\.microbiome$" format="tabular"/> </collection> <collection name="core_microbiome_list" type="list" label="${tool.name} on ${on_string}: core.microbiome list files"> <filter>abundance or samples </filter> <discover_datasets pattern=".*?\.(?P<designation>.*)\.core\.microbiomelist" format="tabular"/> </collection> </outputs> <tests> <test><!-- test with default params --> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <output_collection name="core_microbiome" count="36"> <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with list output and label and group select--> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <param name="abundance" value="30"/> <param name="label" value="0.05,0.22,0.45"/> <param name="group" value="forest,pasture"/> <output_collection name="core_microbiome" count="3"> <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/> </output_collection> <output_collection name="core_microbiome_list" count="3"> <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances. .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome v1.27.0: Updated to Mothur 1.33 ]]></help> <expand macro="citations"/> </tool>