# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1430751537 18000
# Node ID a51980bc0ffe48d16eca21279210ca757f5b39fa
# Parent  9f369b9054471c7f74cd59f284b42545b19a74ac
Add the -show_gis option (NCBI-gis on the NCBI Blast website)

diff -r 9f369b905447 -r a51980bc0ffe tools/blast_plus_remote_blastp.xml
--- a/tools/blast_plus_remote_blastp.xml	Wed Oct 01 21:08:57 2014 -0400
+++ b/tools/blast_plus_remote_blastp.xml	Mon May 04 09:58:57 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0">
+<tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0.1">
     <description>Search protein database with protein query sequence(s)</description>
     <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
     <version_command>blastp -version</version_command>
@@ -43,7 +43,7 @@
 -out blast_output
 ##Set the extended list here so if/when we add things, saved workflows are not affected
 #if str($fmt_opt.out_format)=="text":
-  -outfmt "$fmt_opt.outfmt" $fmt_opt.html
+  -outfmt "$fmt_opt.outfmt" $fmt_opt.html $fmt_opt.show_gis
   #if $fmt_opt.num_descriptions.__str__.strip() != '':
     -num_descriptions $fmt_opt.num_descriptions
   #end if
@@ -162,6 +162,8 @@
                     <option value="4">Flat query-anchored text</option>
                 </param>
                 <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" />
+                <param name="show_gis" type="boolean" label="NCBI-gis" truevalue="-show_gis" falsevalue="" checked="false" 
+                       help="Show the NCBI gis in the Subject def lines"/>
                 <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences.">
                     <validator type="in_range" min="0" />
                 </param>