diff tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 15:c16c30e9ad5b draft

Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)

--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Mon Dec 01 05:59:16 2014 -0500
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Sun Jul 05 10:37:27 2015 -0400
@@ -1,11 +1,11 @@
-<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.01">
+<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.03">
     <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
     <description>masks low complexity regions</description>
     <macros>
         <token name="@BINARY@">dustmasker</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -13,14 +13,13 @@
 #if $db_opts.db_opts_selector == "db":
   -in "${db_opts.database.fields.path}" -infmt blastdb
 #elif $db_opts.db_opts_selector == "histdb":
-  -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb
+  -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
 #else:
   -in "$subject" -infmt fasta
 #end if
 -out "$outfile"
 -window $window -level $level -linker $linker -outfmt $outformat
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="input_conditional_nucleotide_db" />
         <param name="window" type="integer" value="64" label="DUST window length" />
@@ -92,7 +91,7 @@
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please
-cite the following papers (a more specific paper covering this wrapper is planned):
+cite the following papers:
 
 @REFERENCES@
     </help>