Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/heatmap.bin.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
parents | |
children | fcc0778f6987 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/heatmap.bin.xml Tue Jun 07 17:32:23 2011 -0400 @@ -0,0 +1,121 @@ +<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.15.0" 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='$logfile.extra_files_path' + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg' + --READ_cmd='read.otu' + #if $input.source == 'similarity': + --READ_list=$input.otu + #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: + --READ_group='$otu_group' + #end if + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #elif $input.source == 'shared': + --READ_relabund=$input.otu + #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: + --READ_label='$input.label' + #end if + #end if + #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: + --groups=$input.groups + #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> + <!-- get.relabund relabund type should also work --> + <conditional name="input"> + <param name="source" type="select" label="Generate Heatmap for"> + <option value="similarity">OTU list</option> + <option value="relabund">OTU Relative Abundance</option> + </param> + <when value="similarity"> + <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> + <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the 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"/> + </options> + </param> + <param name="groups" type="select" label="groups - Groups to consider" 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> + </when> + <when value="relabund"> + <param name="otu" type="data" format="relabund" label="read.otu(relabund=) - OTU Relative Abundance"/> + <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"/> + </options> + </param> + <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> + <options from_dataset="otu"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="unq_grp" column="1" /> + </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="totalotu">By Total OTUs</option> + <option value="totalgroup">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)"/> + </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. + +.. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin + + </help> +</tool>