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

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

--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -6,11 +6,11 @@
     </macros>
     <expand macro="parallelism" />
     <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
 blastn
--query "$query"
+-query '$query'
 @BLAST_DB_SUBJECT@
 -task $blast_type
 -evalue $evalue_cutoff
@@ -31,9 +31,9 @@
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
         <expand macro="input_conditional_nucleotide_db" />
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
+        <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
             <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
             <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
             <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
@@ -49,16 +49,14 @@
         <expand macro="input_out_format" />
         <expand macro="advanced_options">
             <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
-            <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
+            <param name="filter_query" argument="-dust" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
             <expand macro="input_strand" />
             <expand macro="input_max_hits" />
-            <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" />
-            
+            <param name="identity_cutoff" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" help="Use zero for no cutoff" />
+
             <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
-            <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
-                <validator type="in_range" min="0" />
-            </param>
-            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
+            <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4" />
+            <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
             <expand macro="input_parse_deflines" />
             <expand macro="advanced_optional_id_files" />
             <expand macro="input_qcov_hsp_perc" />
@@ -134,6 +132,15 @@
             <param name="out_format" value="6" />
             <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="query" value="chimera.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="db" />
+            <param name="database" value="rhodopsin_nucs" />
+            <param name="out_format" value="6" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="max_hsps" value="1" />
+            <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" />
+        </test>
         <!-- next test is passing in two blast databases -->
         <test>
             <param name="query" value="chimera.fasta" ftype="fasta" />
@@ -144,7 +151,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**