Mercurial > repos > iuc > mothur_deunique_seqs
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author | iuc |
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date | Mon, 17 Jun 2024 13:11:24 +0000 (5 months ago) |
parents | 3291237294fe |
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<tool profile="16.07" id="mothur_deunique_seqs" name="Deunique.seqs" version="@WRAPPER_VERSION@.0"> <description>Return all sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$fasta' fasta.dat && ln -s '$names' names.dat && echo 'deunique.seqs( #if $inputtype.intype == "countfile": count=names.dat, #else name=names.dat, #end if fasta=fasta.dat )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> <conditional name="inputtype"> <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help=""> <option value="namesfile">names</option> <option value="countfile">count table</option> </param> <when value="namesfile"> <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/> </when> <when value="countfile"> <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/> </when> </conditional> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/> <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information --> <data name="groups_file" format="mothur.groups" from_work_dir="names.redundant.groups" label="${tool.name} on ${on_string}: groups"> <filter>inputtype.intype == 'countfile'</filter> </data> </outputs> <tests> <test><!-- test names file input --> <param name="fasta" value="amazon.unique.fasta"/> <param name="intype" value="namesfile"/> <param name="names" value="amazon.unique.names"/> <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test count file input with group file output --> <param name="fasta" value="amazon.unique.fasta"/> <param name="intype" value="countfile"/> <param name="names" value="amazon_withgroups.count_table"/> <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test count file input without group file output --> <param name="fasta" value="amazon.unique.fasta"/> <param name="intype" value="countfile"/> <param name="names" value="amazon.count_table"/> <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty--> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file. .. _name: https://www.mothur.org/wiki/Name_file .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output ]]></help> <expand macro="citations"/> </tool>