Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/align.check.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_align_check" name="Align.check" version="1.20.0"> <description>Calculate the number of potentially misaligned bases</description> <command interpreter="python"> mothur_wrapper.py --cmd='align.check' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file --outputdir='$logfile.extra_files_path' --fasta=$fasta --map=$ss.map #if $count.__str__ != "None" and len($count.__str__) >0: --count=$count #end if #if $count.__str__ != "None" and len($count.__str__) >0: --name=$name #end if </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/> <conditional name="ss"> <param name="source" label="Select Secondary Structure Map from" type="select"> <option value="cached">Cached Secondary Structure Maps</option> <option value="history">Your History</option> </param> <when value="cached"> <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions"> <options from_data_table="mothur_map"> </options> </param> </when> <when value="history"> <param name="map" format="map" type="data" label="Secondary Structure Map" /> </when> </conditional> <param name="count" type="data" format="count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/> <param name="name" type="data" format="names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/> </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 align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs. .. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map .. _align.check: http://www.mothur.org/wiki/Align.check </help> </tool>