Mercurial > repos > iuc > mothur_list_seqs
view list.seqs.xml @ 1:37a896516dc3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author | iuc |
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date | Tue, 05 Sep 2017 16:58:33 -0400 |
parents | 24044cd8ef87 |
children | 1dcdb5e6c780 |
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<tool profile="16.07" id="mothur_list_seqs" name="List.seqs" version="@WRAPPER_VERSION@.0"> <description>Lists the names (accnos) of the sequences</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 "$search.input" search.input.dat && echo 'list.seqs( #if $search.intype == "fasta": fasta=search.input.dat #elif $search.intype == "fastq": fastq=search.input.dat #elif $search.intype == "name": name=search.input.dat #else if $search.intype == "group": group=search.input.dat #elif $search.intype == "alignreport": alignreport=search.input.dat #elif $search.intype == "list": list=search.input.dat #elif $search.intype == "taxonomy": taxonomy=search.input.dat #elif $search.intype == "count": count=search.input.dat #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <conditional name="search"> <param name="intype" type="select" label="Type to list" help=""> <option value="fasta">Sequence Fasta</option> <option value="fastq">Sequence Fastq</option> <option value="name">Sequences Name reference</option> <option value="group">Groups</option> <option value="alignreport">Align Report</option> <option value="list">OTU List</option> <option value="taxonomy">Sequence Taxonomy</option> <option value="count">Count Table</option> </param> <when value="fasta"> <param name="input" type="data" format="fasta" label="fasta - Fasta"/> </when> <when value="fastq"> <param name="input" type="data" format="fastq" label="fasta - Fasta"/> </when> <when value="name"> <param name="input" type="data" format="mothur.names" label="name - Names"/> </when> <when value="group"> <param name="input" type="data" format="mothur.groups" label="group - Groups"/> </when> <when value="alignreport"> <param name="input" type="data" format="mothur.align.report" label="alignreport - Align Report"/> </when> <when value="list"> <param name="input" type="data" format="mothur.list" label="list - OTU List"/> </when> <when value="taxonomy"> <param name="input" type="data" format="mothur.seq.taxonomy" label="taxonomy - Sequence Taxonomy"/> </when> <when value="count"> <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/> </when> </conditional> </inputs> <outputs> <expand macro="logfile-output"/> <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/> </outputs> <tests> <test><!-- test with fasta --> <param name="intype" value="fasta"/> <param name="input" value="amazon.fasta"/> <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/> <expand macro="logfile-test"/> </test> <test><!-- test with count file --> <param name="intype" value="count"/> <param name="input" value="amazon.count_table"/> <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/> <expand macro="logfile-test"/> </test> </tests> <help> <![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file. .. _name: https://www.mothur.org/wiki/Name_file .. _group: https://www.mothur.org/wiki/Group_file .. _list: https://www.mothur.org/wiki/List_file .. _align.report: https://www.mothur.org/wiki/Align.seqs .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline .. _list.seqs: https://www.mothur.org/wiki/list.seqs v.1.20.0: Updated to mothur 1.33, added count and fastq option ]]> </help> <expand macro="citations"/> </tool>