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

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

--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -3,27 +3,22 @@
     <macros>
         <import>ncbi_macros.xml</import>
     </macros>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
-    <command interpreter="python">
-blastxml_to_tabular.py -o "$tabular_file"
+    <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file'
 #if $output.out_format == "cols":
 #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ")
--c "$cols"
+-c '$cols'
 #else
--c "$output.out_format"
+-c '$output.out_format'
 #end if
-#for i in $blastxml_file#"${i}" #end for#
+#for i in $blastxml_file#'${i}' #end for#
     </command>
     <inputs>
         <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/>
         <conditional name="output">
           <param name="out_format" type="select" label="Output format">
-            <option value="std" selected="True">Tabular (standard 12 columns)</option>
+            <option value="std" selected="true">Tabular (standard 12 columns)</option>
             <option value="ext">Tabular (extended 25 columns)</option>
             <option value="cols">Tabular (select columns to output)</option>
           </param>
@@ -139,7 +134,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of