diff filter_otus_by_sample.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_otus_by_sample.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,32 @@
+<tool id="filter_otus_by_sample" name="filter_otus_by_sample" version="1.2.0">
+ <description>Filter OTU mapping file and sequences by SampleIDs</description>
+ <requirements>
+  <requirement type="binary">filter_otus_by_sample.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  filter_otus_by_sample.py
+  --otu_map_fp=$otu_map_fp
+  --input_fasta_fp=$input_fasta_fp
+  --samples_to_extract=$samples_to_extract
+  --output_dir=$__new_file_path__
+ </command>
+ <inputs>
+  <param name="otu_map_fp" type="data" format="tabular" label="otu_map_fp"
+   help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/>
+  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
+   help="path to the input fasta file [REQUIRED]"/>
+  <param name="samples_to_extract" type="text"  label="samples_to_extract"
+   help="This is a list of sample ids, which should be removed from the OTU file [REQUIRED]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+