Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.groups.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_get_groups" name="Get.groups" version="1.24.0"> <description>Select groups</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($group_in.__str__)) + ":'" + $group_out.__str__] --cmd='get.groups' --outputdir='$logfile.extra_files_path' --group=$group_in #if $groupnames.source == 'groups': #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: --groups=$groupnames.groups #end if #else #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: --accnos=$groupnames.accnos #end if #end if #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 $name_in.__str__ != "None" and len($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__] #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 $shared_in.__str__ != "None" and len($shared_in.__str__) > 0: --shared=$shared_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__] #end if #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: --taxonomy=$taxonomy_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if #if $design_in.__str__ != "None" and len($design_in.__str__) > 0: --design=$design_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($design_in.__str__)) + ":'" + $design_out.__str__] #end if --result=#echo ','.join($results) </command> <inputs> <param name="group_in" type="data" format="groups" label="group - Groups"/> <conditional name="groupnames"> <param name="source" type="select" label="Select Group Names from"> <option value="groups">A List of Group Names</option> <option value="accnos">A History Group Name Accnos Dataset</option> </param> <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"> <options> <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> </when> <when value="accnos"> <param name="accnos" type="data" format="accnos" label="accnos - Group Names from your history"/> </when> </conditional> <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/> <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> <!-- fix format --> <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> <filter>name_in != None</filter> </data> <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> <filter>list_in != None</filter> </data> <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> <filter>shared_in != None</filter> </data> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> <filter>taxonomy_in != None</filter> </data> <data format="design" name="design_out" label="${tool.name} on ${on_string}: pick.design"> <filter>design_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 get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_. .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _list: http://www.mothur.org/wiki/List_file .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _get.groups: http://www.mothur.org/wiki/Get.groups </help> </tool>