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

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

--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -5,7 +5,7 @@
         <import>ncbi_macros.xml</import>
     </macros>
     <expand macro="preamble" />
-    <command>
+    <command detect_errors="aggressive" strict="true">
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"
@@ -13,7 +13,7 @@
 ##TODO: What about -ctrl_a and -target_only as advanced options?
 
 #if $id_opts.id_type=="file":
--entry_batch "$id_opts.entries"
+-entry_batch '$id_opts.entries'
 #else:
 ##Perform some simple search/replaces to remove whitespace
 ##and make it comma separated. Quoted so don't escape pipes.
@@ -40,11 +40,11 @@
 ##using sed, however the exact syntax differs for Mac OS X's sed
 
 #if str($outfmt)=="blastid":
--out "$seq"
+-out '$seq'
 #else if sys.platform == "darwin":
-| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq"
+| sed -E 's/^&gt;(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/&gt;/1' &gt; "$seq"
 #else:
-| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
+| sed 's/&gt;\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/&gt;/1' &gt; "$seq"
 #end if
     </command>
     <inputs>
@@ -55,10 +55,10 @@
               <option value="prompt">User entered</option>
             </param>
             <when value="file">
-                <param name="entries" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/>
+                <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/>
             </when>
             <when value="prompt">
-                <param name="entries" type="text" label="Sequence identifier(s)" help="Comma or new line separated list." optional="False" area="True" size="10x30"/>
+                <param name="entries" argument="-entry" type="text" optional="false" area="true" size="10x30" label="Sequence identifier(s)" help="Comma or new line separated list"/>
             </when>
         </conditional>
         <param name="outfmt" type="select" label="Output format">
@@ -105,7 +105,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 Extracts FASTA formatted sequences from a BLAST database
@@ -138,5 +138,5 @@
 
 @REFERENCES@
     </help>
-    <expand macro="blast_citations" />    
+    <expand macro="blast_citations" />
 </tool>