Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/degap.seqs.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_degap_seqs" name="Degap.seqs" version="1.20.0"> <description>Remove gap characters from sequences</description> <command interpreter="python"> mothur_wrapper.py --cmd='degap.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.ng\.\w+$:'$out_fasta --outputdir='$logfile.extra_files_path' --fasta=$fasta </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> <requirement type="package" version="1.27">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 degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed. .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs </help> </tool>