diff summarize_taxa.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_taxa.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,42 @@
+<tool id="summarize_taxa" name="summarize_taxa" version="1.2.1">
+ <description>Summarize Taxa</description>
+ <requirements>
+  <requirement type="binary">summarize_taxa.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  summarize_taxa.py
+  --otu_table_fp=$otu_table_fp
+  --output_fp=$output_fp
+  --level=$level
+  #if $mapping != None and $mapping.__str__ != 'None':
+   --mapping=$mapping
+  #end if
+  #if $delimiter != ';':
+   --delimiter=$delimiter
+  #end if
+  ## --relative_abundance=$relative_abundance
+  $absolute_abundance
+ </command>
+ <inputs>
+  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
+   help="Path to read otu file [REQUIRED]"/>
+  <param name="level" type="integer" value="2" label="level"
+   help="Level of taxonomy to use [default: 2]"/>
+  <param name="mapping" type="data" format="qiimemapping" optional="true" label="mapping"
+   help="if supplied - the taxon information will be added to the mapping file. This mapping file can be used to color PCoA plots by taxon abundance or to perform statistical tests of taxon/mappingy associations."/>
+  <param name="delimiter" type="text" value="\;" label="delimiter"
+   help="Delimitor that separates taxonomy categories.[default: ;]"/>
+  <param name="absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="absolute_abundance"
+   help="If present, reports the absolute abundance of the lineage in each sample. By default uses relative abundance [default: False]"/>
+ </inputs>
+ <outputs>
+  <data format="qiimetaxsummary" name="output_fp" label="${tool.name} on ${on_string}: taxa_summary"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+