# HG changeset patch
# User galaxyp
# Date 1412211137 14400
# Node ID db990c5edc149e2569cb8ae3e7ac78448af0d848
# Parent  820c41bff4625dbbc9ea826a1ecc12e8c0717e0b
Uploaded

diff -r 820c41bff462 -r db990c5edc14 tools/blast_plus_remote_blastp.xml
--- a/tools/blast_plus_remote_blastp.xml	Wed Oct 01 20:47:55 2014 -0400
+++ b/tools/blast_plus_remote_blastp.xml	Wed Oct 01 20:52:17 2014 -0400
@@ -1,6 +1,5 @@
 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0">
     <description>Search protein database with protein query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into four (This only works if output is tabular) -->
     <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>
     <requirements>
@@ -177,7 +176,6 @@
             </param>
             <when value="basic" />
             <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
                 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
                 <conditional name="scoring">
                     <param name="matrix" type="select" label="Scoring matrix">
@@ -312,15 +310,8 @@
                             <option value="-gapopen 8 -gapextend 1">Existense: 8  Extension: 1</option>
                         </param>
                     </when>
-                <!--
-                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 blastp 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" />
-                -->
                 </conditional>
 
-                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
                 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
                     <validator type="in_range" min="2" />
                 </param>