diff preprocessing.xml @ 3:221a97bf686d draft

Uploaded

--- a/preprocessing.xml	Thu Feb 26 19:31:20 2015 -0500
+++ b/preprocessing.xml	Wed Mar 25 16:39:10 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0">
-  <description>in preparation for phylogenetic placement</description>
+<tool id="PHYLO_preprocessing" name="Deduplicate sequences" version="3.0.0">
+  <description>in preparation for alignment and placement</description>
   <requirements>
     <requirement type="package">yapp_env</requirement>
   </requirements>
@@ -14,26 +14,20 @@
     <expand macro="basic_errors"/>
   </stdio>
   <inputs>
-    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
     <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
     <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
   </inputs>
   <outputs>
     <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/>
     <data name="dedup_info" format="csv" label="Deduplication info"/>
-    <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
-    <data name="aligned_scores" format="txt" label="Alignment scores"/>
   </outputs>
   <configfiles>
     <configfile name="config">
-REFPKG="${refpkg.extra_files_path}"
 INPUT_SEQS="${input_seqs}"
 SPLIT_MAP="${split_map}"
 
 DEDUP_SEQS="${dedup_seqs}"
 DEDUP_INFO="${dedup_info}"
-ALIGNED_SEQS="${aligned_seqs}"
-ALIGNED_SCORES="${aligned_scores}"
     </configfile>
   </configfiles>
   <!-- The contents of the help tag is parsed as reStructuredText. Please see
@@ -45,9 +39,7 @@
 
 **What it does**
 
-This tool aligns query sequences with the reference sequences used to make the
-reference tree contained in the reference package and then merges the query and
-reference sequences.
+This tool deduplicates input sequences in preparation for alignment and placement.
 
   </help>
 </tool>