Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/chimera.perseus.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> |
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date | Wed, 04 Sep 2013 10:51:34 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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31:a3eed59297ea | 32:ec8df51e841a |
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2 <description>Find putative chimeras using chimeraCheck</description> | 2 <description>Find putative chimeras using chimeraCheck</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='chimera.perseus' | 5 --cmd='chimera.perseus' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file |
7 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos | |
7 --outputdir='$logfile.extra_files_path' | 8 --outputdir='$logfile.extra_files_path' |
8 --fasta=$fasta | 9 --fasta=$fasta |
9 --name=$name | 10 --name=$name |
10 #if $group.__str__ != "None" and len($group.__str__) > 0: | 11 #if $group.__str__ != "None" and len($group.__str__) > 0: |
11 --group='$group' | 12 --group='$group' |
30 <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> | 31 <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> |
31 </inputs> | 32 </inputs> |
32 <outputs> | 33 <outputs> |
33 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 34 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
34 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> | 35 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> |
36 <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" /> | |
35 </outputs> | 37 </outputs> |
36 <requirements> | 38 <requirements> |
37 <requirement type="package" version="1.27">mothur</requirement> | 39 <requirement type="package" version="1.27">mothur</requirement> |
38 </requirements> | 40 </requirements> |
39 <tests> | 41 <tests> |