Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/merge.files.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_merge_files" name="Merge.files" version="1.19.0"> <description>Merge data</description> <command interpreter="python"> mothur_wrapper.py --cmd='merge.files' --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output --outputdir='$logfile.extra_files_path' --input=${merge.input}#for i in $merge.inputs#,${i.input}#end for# --output='mergefile' </command> <inputs> <conditional name="merge"> <param name="type" type="select" format="fasta,qual,groups,names,accnos" label="Merge"> <option value="fasta">fasta</option> <option value="qual">qual</option> <option value="groups">groups</option> <option value="names">names</option> <option value="accnos">accnos</option> </param> <when value="fasta"> <param name="input" type="data" format="fasta" label="input - fasta"/> <repeat name="inputs" title="And fasta"> <param name="input" type="data" format="fasta" label="input - fasta"/> </repeat> </when> <!-- fasta --> <when value="qual"> <param name="input" type="data" format="qual" label="input - qual"/> <repeat name="inputs" title="And qual"> <param name="input" type="data" format="qual" label="input - qual"/> </repeat> </when> <!-- qual --> <when value="groups"> <param name="input" type="data" format="groups" label="input - groups"/> <repeat name="inputs" title="And group"> <param name="input" type="data" format="groups" label="input - groups"/> </repeat> </when> <!-- groups --> <when value="names"> <param name="input" type="data" format="names" label="input - names"/> <repeat name="inputs" title="And name"> <param name="input" type="data" format="names" label="input - names"/> </repeat> </when> <!-- names --> <when value="accnos"> <param name="input" type="data" format="accnos" label="input - accnos"/> <repeat name="inputs" title="And accno"> <param name="input" type="data" format="accnos" label="input - accnos"/> </repeat> </when> <!-- fasta --> </conditional> <!-- merge --> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/> </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 merge.files_ command merge inputs into a single output. .. _merge.files: http://www.mothur.org/wiki/Merge.files </help> </tool>