Mercurial > repos > iuc > mothur_create_database
view create.database.xml @ 9:16f6d606521a draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author | iuc |
---|---|
date | Fri, 22 Jan 2021 00:28:15 +0000 |
parents | 024a52bdf70c |
children |
line wrap: on
line source
<tool profile="16.07" id="mothur_create_database" name="Create.database" version="@WRAPPER_VERSION@.0"> <description>creates a database file from a list, repnames, repfasta and contaxonomy file</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 '$otu' otu.dat && ln -s '$repfasta' repfasta.dat && ln -s '$nameOrCount' nameOrCount.dat && ln -s '$constaxonomy' constaxonomy.dat && ln -s '$group' group.dat && echo 'create.database( #if $otu.is_of_type("mothur.list"): list=otu.dat #elif $otu.is_of_type("mothur.shared"): shared=otu.dat #end if ,repfasta=repfasta.dat #if $nameOrCount.is_of_type("mothur.names"): ,repname=nameOrCount.dat #elif $nameOrCount.is_of_type("mothur.count_table"): ,count=nameOrCount.dat #end if ,constaxonomy=constaxonomy.dat #if $group: ,group=group.dat #end if #if $label: ,label=$label #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/> <param name="repfasta" type="data" format="fasta" optional="true" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/> <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="repname/count - Representative sequences" help="rep.name file or rep.count_table file generated by get.oturep"/> <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/> <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> <param name="label" type="select" label="label - OTU Labels" optional="true" help="Select exactly one label. If none selected, first label in your list or shared file will be used"> <expand macro="labeloptions"/> </param> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/> </outputs> <tests> <!-- Test with a mothur.names file --> <test> <param name="otu" value="cd-test.list" ftype="mothur.list"/> <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/> <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> <param name="label" value="unique"/> <output name="database" file="cd-test.database" ftype="tabular"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <!-- Test with a mothur.count_table file --> <test> <param name="otu" value="cd-test.list" ftype="mothur.list"/> <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/> <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> <param name="label" value="unique"/> <output name="database" file="cd-test.database" ftype="tabular"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. .. _list: https://www.mothur.org/wiki/List_file .. _shared: https://www.mothur.org/wiki/Shared_file .. _create.database: https://www.mothur.org/wiki/Create.database v.1.28.0: Updated to Mothur 1.33, added count paramter. ]]></help> <expand macro="citations"/> </tool>