diff filter_otu_table.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_otu_table.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,43 @@
+<tool id="filter_otu_table" name="filter_otu_table" version="1.2.0">
+ <description>Filters OTU table by minimum OTU count and number of samples or by taxonomy</description>
+ <requirements>
+  <requirement type="binary">filter_otu_table.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  filter_otu_table.py
+  --otu_table_fp=$otu_table_fp
+  --min_count=$min_count
+  --min_samples=$min_samples
+  --include_taxonomy=$include_taxonomy
+  --exclude_taxonomy=$exclude_taxonomy
+  --dir_path=$dir_path
+  --seqs_per_sample=$seqs_per_sample
+ </command>
+ <inputs>
+  <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
+   help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
+  <param name="min_count" type="integer" value="1" label="min_count"
+   help="retain OTUs with at least this many sequences [default=1]"/>
+  <param name="min_samples" type="integer" value="2" label="min_samples"
+   help="retain OTUs found in at least this many samples [default=2]"/>
+  <param name="include_taxonomy" type="text" value="" label="include_taxonomy"
+   help="list of taxonomy terms to include [default=]"/>
+  <param name="exclude_taxonomy" type="text" value="" label="exclude_taxonomy"
+   help="list of taxonomy terms to exclude [default=]"/>
+  <param name="dir_path" type="text" value="./" label="dir_path"
+   help="directory prefix for all analyses [default=./]"/>
+  <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
+   help="minimum sequences per sample to retain the sample. [default=('NO', 'DEFAULT')]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+