Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/make.group.xml @ 32:ec8df51e841a
Fixes courtesy of Peter Briggs:
metagenomics.py:
- Groups class: Fix for when second column not present
- Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular
data uploads being sniffed as this type
mothur_wrapper.py:
- update cmd_dict['chimera.perseus'], to use correct inputs
- add --beta option (needed for chimera.perseus tool)
- add function for converting input floats from scientific notation (e.g. 1e-6,
which mothur can't handle) to decimal format (e.g. 0.00001, which it can)
chimera.perseus.xml:
- add output data item for the "accnos" file (not previous captured in the
history)
trim.flows.xml:
- cosmetic change: base name for additional output data items is now "trim.flows",
rather than "logfile" (clarifies history items)
shhh.flows.xml:
- cosmetic change: update default value specified in help for mindiff to be
consistent with that given in the mothur documentation
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 04 Sep 2013 10:51:34 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_make_files" name="Make.group" version="1.19.0"> <description>Make a group file</description> <command interpreter="python"> mothur_wrapper.py --cmd='make.group' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.group:'$output --outputdir='$logfile.extra_files_path' --fasta=${fasta}#for i in $inputs#,${i.fasta}#end for# --groups=${group}#for i in $inputs#,${i.group}#end for# </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/> <param name="group" type="text" label="group - Group name"/> <repeat name="inputs" title="Additional"> <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/> <param name="group" type="text" label="group - Group name"/> </repeat> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="groups" name="output" label="${tool.name} on ${on_string}: group" /> </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 make.group_ command reads a fasta file or series of fasta files and creates a group_ file. .. _group: http://www.mothur.org/wiki/Group_file .. _make.group: http://www.mothur.org/wiki/Make.group </help> </tool>