diff pick_rep_set.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pick_rep_set.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,47 @@
+<tool id="pick_rep_set" name="pick_rep_set" version="1.2.1">
+ <description>Pick representative set of sequences</description>
+ <requirements>
+  <requirement type="binary">pick_rep_set.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  pick_rep_set.py
+  --input_file=$input_file
+  --fasta_file=$fasta_file
+  --rep_set_picking_method=$rep_set_picking_method
+  --sort_by=$sort_by
+  --reference_seqs_fp=$reference_seqs_fp
+  --log_fp=$log_fp
+  --result_fp=$result_fp
+ </command>
+ <inputs>
+  <param name="input_file" type="data" format="qiimeotu" label="input_file"
+   help="Path to input otu mapping file [REQUIRED]"/>
+  <param name="reference_seqs_fp" type="data" format="fasta" optional="true" label="reference_seqs_fp"
+   help="collection of preferred representative sequences [default: ('NO', 'DEFAULT')]"/>
+  <param name="fasta_file" type="data" format="fasta" optional="true" label="fasta_file"
+   help="Path to input fasta file [REQUIRED if not picking against a reference set; default: None]"/>
+  <param name="rep_set_picking_method" type="select" label="rep_set_picking_method"
+   help="Method for picking representative sets.  Valid choices are random, longest, most_abundant, first[default: first]">
+    <option value="random">random</option>
+    <option value="longest">longest</option>
+    <option value="most_abundant">most_abundant</option>
+    <option value="first" selected="true">first</option>
+  </param>
+  <param name="sort_by" type="select" value="otu" label="sort_by" >
+    <option value="otu" selected="true">otu</option>
+    <option value="seq_id">seq_id</option>
+  </param>
+
+ </inputs>
+ <outputs>
+   <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
+   <data format="fasta" name="result_fp" label="${tool.name} on ${on_string}: rep_set.fasta" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+