diff tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @ 22:6f386c5dc4fb draft

v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates

--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -6,11 +6,11 @@
     </macros>
     <expand macro="parallelism" />
     <expand macro="preamble" />
-    <command>
+    <command detect_errors="aggressive">
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 tblastn
--query "$query"
+-query '$query'
 @BLAST_DB_SUBJECT@
 -task $blast_type
 -evalue $evalue_cutoff
@@ -30,10 +30,10 @@
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/>
 
         <expand macro="input_conditional_nucleotide_db" />
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
+        <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
             <option value="tblastn">tblastn - Traditional TBLASTN to compare protein query to translated nucleotide database</option>
             <option value="tblastn-fast">tblastn-fast - Use longer words for seeding, faster but less accurate</option>
         </param>
@@ -51,7 +51,7 @@
             Can't use '-ungapped' on its own, error back is:
             Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
             Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
-            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
+            <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
             -->
             <expand macro="input_parse_deflines" />
             <expand macro="advanced_optional_id_files" />
@@ -144,7 +144,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**