Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/list.seqs.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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<tool id="mothur_list_seqs" name="List.seqs" version="1.20.0"> <description>Lists the names (accnos) of the sequences</description> <command interpreter="python"> mothur_wrapper.py --cmd='list.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.accnos$:'$out_file --outputdir='$logfile.extra_files_path' #if $search.type == "fasta": --fasta=$search.input #elif $search.type == "name": --name=$search.input #else if $search.type == "group": --group=$search.input #elif $search.type == "alignreport": --alignreport=$search.input #elif $search.type == "list": --list=$search.input #elif $search.type == "taxonomy": --taxonomy=$search.input #end if #if $count.__str__ != "None" and len($count.__str__) > 0: --count=$count #end if </command> <inputs> <conditional name="search"> <param name="type" type="select" label="Type to list" help=""> <option value="fasta">Sequence Fasta</option> <option value="name">Sequences Name reference</option> <option value="group">Groups</option> <option value="alignreport">Align Report</option> <option value="list">OTU List</option> <option value="taxonomy">Sequence Taxonomy</option> </param> <when value="fasta"> <param name="input" type="data" format="fasta" label="fasta - Fasta"/> </when> <when value="name"> <param name="input" type="data" format="names" label="name - Names"/> </when> <when value="group"> <param name="input" type="data" format="groups" label="group - Groups"/> </when> <when value="alignreport"> <param name="input" type="data" format="align.report" label="alignreport - Align Report"/> </when> <when value="list"> <param name="input" type="data" format="list" label="list - OTU List"/> </when> <when value="taxonomy"> <param name="input" type="data" format="seq.taxonomy" label="taxonomy - Sequence Taxonomy"/> </when> </conditional> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="count" type="data" format="fastq" optional="true" label="fastq"/> </inputs> <outputs> <!-- fix format --> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="accnos" name="out_file" label="${tool.name} on ${on_string}: accnos" /> </outputs> <requirements> <requirement type = "package" version ="1.33">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file. .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _list: http://www.mothur.org/wiki/List_file .. _align.report: http://www.mothur.org/wiki/Align.seqs .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _list.seqs: http://www.mothur.org/wiki/list.seqs v.1.20.0: Updated to mothur 1.33, added count and fastq option </help> </tool>