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

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

--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -5,18 +5,18 @@
         <import>ncbi_macros.xml</import>
     </macros>
     <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
 segmasker
 #if $db_opts.db_opts_selector == "db":
-  -in "${db_opts.database.fields.path}" -infmt blastdb
+  -in '${db_opts.database.fields.path}' -infmt blastdb
 #elif $db_opts.db_opts_selector == "histdb":
-  -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
+  -in '${os.path.join($db_opts.histdb.files_path, "blastdb")}' -infmt blastdb
 #else:
-  -in "$subject" -infmt fasta
+  -in '$subject' -infmt fasta
 #end if
--out "$outfile"
+-out '$outfile'
 -window $window
 -locut $locut
 -hicut $hicut
@@ -42,9 +42,9 @@
             <change_format>
                 <when input="outformat" value="fasta" format="fasta" />
                 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" />
-		<!--
+                <!--
                 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" />
-		-->
+                -->
                 <when input="outformat" value="maskinfo_xml" format="xml" />
             </change_format>
         </data>