view qiime/summarize_taxa.xml @ 6:d1cf2064ddd8 draft default tip

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<tool id="summarize_taxa" name="summarize_taxa" version="2.0.0" force_history_refresh="True">
<description>Summarize Taxa</description>
 <requirements>
  <requirement type="binary">summarize_taxa.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  #set $levelnums = str($level).split(",")
  #set $filestr = ""
  #if $len($level.__str__) > 1:
  #for $i in $levelnums:
  #set $filestr = $filestr + '^\\\\S+_L'+$i+'\\\\.txt$:txt,'
  #end for
  --galaxy_new_datasets=$filestr
  --galaxy_datasetid=$output1.id
  --galaxy_new_files_path='$__new_file_path__'
  --galaxy_logfile=$output1.__str__
  #else:
  --galaxy_datasets='^\S+_L'$level'\.txt$:'$output1
  --galaxy_outputdir='$output1.extra_files_path'
  #end if
  summarize_taxa.py
  --otu_table_fp=$otu_table_fp
  --level=$level
  #if $mapping != None and $mapping.__str__ != 'None':
  --mapping=$mapping
  #end if
  #if $len($level.__str__) > 1:
  --output_dir=$__new_file_path__
  #else:
  --output_dir='$output1.extra_files_path'
  #end if
  $absolute_abundance
  #if $lower_percentage > 0.0 and $lower_percentage.__str__ != '':
  --lower_percentage=$lower_percentage
  #end if
  #if $upper_percentage > 0.0 and $upper_percentage.__str__ != '':
  --upper_percentage=$upper_percentage
  #end if
  $transposed_output
  #if $delimiter.__str__ != ';':
  --delimiter=$delimiter
  #end if
 </command>
 <!--
 '^\S+_log\.txt$:'$log
 \'$__collected_datasets_primary_output$i
 galaxy_outputdir='$__new_file_path__'
 -->
 <inputs>
  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
   help="Input OTU table [REQUIRED]"/>
  <param name="level" type="text" value="2,3,4,5,6" label="level"
   help="Level of taxonomy to use [default: 2,3,4,5,6]"/>
  <param name="mapping" type="data" format="qiimemapping" optional="true" label="mapping"
   help="if supplied - the taxon information will be added to the mapping file. This mapping file can be used to color PCoA plots by taxon abundance or to perform statistical tests of taxon/mapping associations. If you plan to plot your taxa summaries, do not upload a mapping file."/>
  <param name="delimiter" type="text" value=";" label="delimiter"
   help="Delimiter that separates taxonomy categories. [default: ;]">
    <sanitizer sanitize="False">
   <valid>
     <add value=";"/>
     <add value="|"/>
    </valid>
 </sanitizer>
 </param>
  <param name="absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="absolute_abundance"
   help="If present, reports the absolute abundance of the lineage in each sample. By default uses relative abundance [default: False]"/>
   <param name="lower_percentage" type="float" optional="true" value="" label="lower_percentage"
   help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05. [default: None]"/>
  <param name="upper_percentage" type="float" optional="true" value="" label="upper_percentage"
   help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45. [default: None]"/>
  <param name="transposed_output" type="boolean" truevalue="--transposed_output" falsevalue="" checked="false" label="transposed_output"
   help="If present, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data [default: False]"/>
 </inputs>
 <outputs>
  <data format="txt" name="output1" label="${tool.name} on ${on_string}: taxa_summary for Level $level"/>
 </outputs>
 <tests>
 </tests>
 <help>
.. class:: warningmark

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For more information, see summarize_taxa_ in the Qiime documentation.
 
Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
 
 .. _summarize_taxa: http://qiime.org/scripts/summarize_taxa.html</help>
</tool>