diff otu_category_significance.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/otu_category_significance.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,44 @@
+<tool id="otu_category_significance" name="otu_category_significance" version="1.2.0">
+ <description>OTU significance and co-occurence analysis</description>
+ <requirements>
+  <requirement type="binary">otu_category_significance.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  otu_category_significance.py
+  --otu_table_fp=$otu_table_fp
+  --category_mapping_fp=$category_mapping_fp
+  --category=$category
+  --test=$test
+  --output_fp=$output_fp
+  --filter=$filter
+  --threshold=$threshold
+  --otu_include_fp=$otu_include_fp
+ </command>
+ <inputs>
+  <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
+   help="path to the otu table, or to a directory containing OTU tables [REQUIRED]"/>
+  <param name="category_mapping_fp" type="data" format="tabular" label="category_mapping_fp"
+   help="path to category mapping file [REQUIRED]"/>
+  <param name="category" type="text"  label="category"
+   help="name of category over which to run the analysis [REQUIRED]"/>
+  <param name="test" type="text" value="g_test" label="test"
+   help="the type of statistical test to run. options are: g_test: determines whether OTU presence/absence is associated with a category using the G test of independence. ANOVA: determines whether OTU abundance is associated with a category. correlation: determines whether OTU abundance is correlated with a continuous variable in the category mapping file."/>
+  <param name="filter" type="text" value="10" label="filter"
+   help="minimum number of samples that must contain the OTU for the OTU to be included in the analysis. default value=10."/>
+  <param name="threshold" type="text"  label="threshold"
+   help="threshold under which to consider something absent: Only used if you have numerical data that should be converted to present or absent based on a threshold. Should be None for categorical data or with the correlation test. default value is None"/>
+  <param name="otu_include_fp" type="data" format="txt" label="otu_include_fp"
+   help="path to a file with a list of OTUs to evaluate. By default evaluates all OTUs that pass the minimum sample filter. If a filepath is given here in which each OTU name one wishes to evaluate is on a separate line, will apply this additional filter"/>
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fp"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+