Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/heatmap.bin.xml @ 11:11867a45a43d
Change make.shared param name from unique to groups
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 14 Jul 2011 15:21:01 -0500 |
parents | 7bfe1f843858 |
children | bfbaf823be4c |
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<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.20.0" force_history_refresh="True"> <description>Generate a heatmap for OTUs</description> <command interpreter="python"> mothur_wrapper.py --cmd='heatmap.bin' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg' #end if #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$input.otu #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): --rabund=$input.otu #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): --sabund=$input.otu #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): --list=$input.otu #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): --relabund=$input.otu #end if #if $input.has_groups != 'no' and $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --groups=$input.groups #end if #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --label='$input.label' #end if #if $scale.__str__ != "None" and len($scale.__str__) > 0: --scale='$scale' #end if #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: --sorted='$sorted' #end if #if $numotu > 0: --numotu=$numotu #end if #if 100 > $fontsize > 0: --fontsize=$fontsize #end if </command> <inputs> <conditional name="input"> <param name="has_groups" type="select" label="Generate Heatmap for"> <option value="default">shared or relabund</option> <option value="no">list, rabund, sabund</option> <option value="yes">list, rabund, sabund with groups</option> </param> <when value="default"> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU List"/> <param name="groups" type="select" label="groups - Groups to condider" multiple="true"> <options from_dataset="otu"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> </when> <when value="no"> <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> </when> <when value="yes"> <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/> <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> <options from_dataset="otu_group"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> </when> </conditional> <param name="scale" type="select" label="scale - Scaling for heatmap"> <option value="">Default</option> <option value="log10">Log10</option> <option value="log2">Log2</option> <option value="linear">Linear</option> </param> <param name="sorted" type="select" label="sorted - Sort heatmap"> <option value="">By shared</option> <option value="none">Don't sort</option> <option value="topotu">By Total OTUs</option> <option value="topgroup">By Total Groups</option> </param> <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/> <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> <requirement type="binary">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 heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file. .. _list: http://www.mothur.org/wiki/List_file .. _shared: http://www.mothur.org/wiki/Shared_file .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin </help> </tool>