Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/remove.lineage.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_remove_lineage" name="Remove.lineage" version="1.20.0"> <description>Picks by taxon</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] --cmd='remove.lineage' --outputdir='$logfile.extra_files_path' --taxonomy=$taxonomy --taxon="'$re.sub('(\s|,)+',',',$re.sub('\(\d+\)','',$taxon.value.__str__))'" #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: --fasta=$fasta_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] #end if #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: --group=$group_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] #end if #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0: --alignreport=$alignreport_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.pick.align.report',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__] #end if #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: --list=$list_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] #end if #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: --name=$name_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] $dups #end if --result=#echo ','.join($results) </command> <inputs> <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> <!-- <param name="taxons" type="select" size="120" multiple="true" label="Browse Taxons from Taxonomy"> <options from_dataset="taxonomy"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unique_taxon" column="1" /> <filter type="sort_by" name="sorted_taxon" column="1" /> </options> </param> --> <param name="taxon" type="text" area="True" size="5x120" label="taxon - Select Taxons for filtering" help="Enter 1 or more taxons separated by whitespace or commas"/> <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> <param name="group_in" type="data" format="groups" optional="true" label="group - Groups"/> <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/> <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group"> <filter>group_in != None</filter> </data> <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> <filter>list_in != None</filter> </data> <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> <filter>name_in != None</filter> </data> <data format="align.report" name="alignreport_out" label="${tool.name} on ${on_string}: pick.align.report"> <filter>alignreport_in != None</filter> </data> </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 remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences. .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _list: http://www.mothur.org/wiki/List_file .. _align.report: http://www.mothur.org/wiki/Align.seqs .. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage </help> </tool>