Mercurial > repos > iuc > mothur_get_otus
view get.otus.xml @ 3:009304a59939 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 04:17:37 -0400 |
parents | 04a479ceb84a |
children | 3f68e8e700c9 |
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<tool profile="16.07" id="mothur_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0"> <description>Get otus containing sequences from specified groups</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 '$accnos' accnos.dat && #if $list: ln -s '$list' list.dat && #end if #if $shared: ln -s '$shared' shared.dat && #end if #if $constaxonomy: ln -s '$constaxonomy' constaxonomy.dat && #end if #if $corraxes: ln -s '$corraxes' corraxes.dat && #end if #if $otucorr: ln -s '$otucorr' otucorr.dat && #end if echo 'get.otus( #if $list list=list.dat, #end if #if $shared shared=shared.dat, #end if #if $corraxes: corraxes=corraxes.dat, #end if #if $otucorr: otucorr=otucorr.dat, #end if #if $constaxonomy constaxonomy=constaxonomy.dat, #end if accnos=accnos.dat #if $labelsource.label: ,label=${ str($labelsource.label).replace(",","-") } #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param argument="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/> <param argument="list" type="data" format="mothur.list" optional="true" label="OTU List"/> <param argument="shared" type="data" format="mothur.shared" optional="true" label="OTU List OTU Shared file"/> <param argument="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" help="The contaxonomy file is the taxonomy file outputted by classify.otu"/> <param argument="otucorr" type="data" format="mothur.otu.corr" optional="true" label="OTU correlation file" help="otu correlation coefficients are output by the otu.association command"/> <param argument="corraxes" type="data" format="mothur.axes" optional="true" label="Correlation axes file" help="correlation axes file is output by the corr.axes command"/> <conditional name="labelsource"> <param name="source" type="select" label="Select a label from"> <option value="list"> OTU list file </option> <option value="shared"> OTU shared file </option> </param> <when value="list"> <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used"> <options> <filter type="data_meta" ref="list" key="labels"/> </options> </param> </when> <when value="shared"> <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used"> <options> <filter type="data_meta" ref="shared" key="labels"/> </options> </param> </when> </conditional> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="list_out" format="mothur.list" from_work_dir="list*.pick.*" label="${tool.name} on ${on_string}: pick.list"> <filter> $list </filter> </data> <data name="shared_out" format="mothur.shared" from_work_dir="shared*.pick.*" label="${tool.name} on ${on_string}: pick.shared"> <filter> $shared </filter> </data> <data name="constaxonomy_out" format="mothur.cons.taxonomy" from_work_dir="constaxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> <filter> $constaxonomy </filter> </data> <data name="otucorr_out" format="mothur.otu.corr" from_work_dir="otucorr*.pick.*" label="${tool.name} on ${on_string}: pick.otu.corr"> <filter> $otucorr </filter> </data> <data name="corraxes_out" format="mothur.axes" from_work_dir="corraxes*.pick.*" label="${tool.name} on ${on_string}: pick.axes"> <filter> $corraxes </filter> </data> </outputs> <tests> <test><!-- test with list file input and default settings --> <param name="list" value="amazon.an.list" ftype="mothur.list"/> <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/> <output name="list_out" ftype="mothur.list"> <assert_contents> <expand macro="test-list-format"/> <has_text text="unique"/> <has_text text="Otu01"/> <has_text text="Otu17"/> <has_text text="Otu42"/> <not_has_text text="Otu43"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with shared and otu.corr file and label select --> <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/> <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/> <param name="label" value="0.03"/> <param name="source" value="shared"/> <param name="otucorr" value="amazon.an.0.03.pearson.otu.corr" ftype="mothur.cons.taxonomy"/> <output name="shared_out" ftype="mothur.shared"> <assert_contents> <expand macro="test-shared-format"/> <has_text text="0.03"/> <has_text text="Otu01"/> <has_text text="Otu17"/> <has_text text="Otu42"/> <not_has_text text="Otu43"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The get.otus command selects otus from a given list. .. _list: https://www.mothur.org/wiki/List_file .. _get.otus: https://www.mothur.org/wiki/Get.otus ]]></help> <expand macro="citations"/> </tool>