diff single_rarefaction.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/single_rarefaction.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,34 @@
+<tool id="single_rarefaction" name="single_rarefaction" version="1.2.0">
+ <description>Perform rarefaction on an otu table</description>
+ <requirements>
+  <requirement type="binary">single_rarefaction.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  single_rarefaction.py
+  --input_path=$input_path
+  --output_path=$output_path
+  --depth=$depth
+  $lineages_included
+  $keep_empty_otus
+ </command>
+ <inputs>
+  <param name="input_path" type="qiimeotutable"  label="input_path"
+   help="input otu table filepath [REQUIRED]"/>
+  <param name="depth" type="integer" value="-1" label="depth"
+   help="sequences per sample to subsample [REQUIRED]"/>
+  <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
+   help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
+  <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
+   help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/>
+ </inputs>
+ <outputs>
+  <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+