diff tools/ncbi_blast_plus/ncbi_segmasker_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_segmasker_wrapper.xml	Mon Dec 01 05:59:16 2014 -0500
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Sun Jul 05 10:37:27 2015 -0400
@@ -1,10 +1,10 @@
-<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.01">
+<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.03">
     <description>low-complexity regions in protein sequences</description>
     <macros>
         <token name="@BINARY@">segmasker</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
@@ -12,7 +12,7 @@
 #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
@@ -22,7 +22,6 @@
 -hicut $hicut
 -outfmt $outformat
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="input_conditional_protein_db" />
         <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" />
@@ -94,7 +93,7 @@
 **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>