annotate summarize_otu_by_cat.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="summarize_otu_by_cat" name="summarize_otu_by_cat" version="1.2.0">
 <description>Create a summarized OTU table for a specific metadata category</description>
 <requirements>
  <requirement type="binary">summarize_otu_by_cat.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  summarize_otu_by_cat.py
  --input_map=$input_map
  --otu_file=$otu_file
  --meta_category=$meta_category
  --dir-prefix=$dir_prefix
  $normalize_flag
 </command>
 <inputs>
  <param name="input_map" type="data" format="tabular" label="input_map"
   help="name of input map file [REQUIRED]"/>
  <param name="otu_file" type="data" format="txt" label="otu_file"
   help="name of otu table file [REQUIRED]"/>
  <param name="meta_category" type="text"  label="meta_category"
   help="name of category for OTU table [REQUIRED]"/>
  <param name="dir_prefix" type="text"  label="dir-prefix"
   help="directory prefix for all analyses [default: cwd]"/>
  <param name="normalize_flag" type="boolean" truevalue="--normalize_flag" falsevalue="" checked="false" label="normalize_flag"
   help="if True will normalize counts [default: False]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>