diff tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 9:9dabbfd73c8a draft

Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database. Also includes other minor improvements.

--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Feb 19 12:49:43 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Thu Apr 25 09:38:37 2013 -0400
@@ -1,7 +1,11 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.17">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.19">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">blastn</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>blastn -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -17,7 +21,7 @@
 #end if
 -task $blast_type
 -evalue $evalue_cutoff
--out $output1
+-out "$output1"
 ##Set the extended list here so if/when we add things, saved workflows are not affected
 #if str($out_format)=="ext":
     -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
@@ -47,13 +51,13 @@
         <exit_code range=":-1" />
         <!-- In case the return code has not been set propery check stderr too -->
         <regex match="Error:" />
-        <regex match="EXception:" />
+        <regex match="Exception:" />
     </stdio>
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
+              <option value="db" selected="True">Locally installed BLAST database</option>
               <option value="histdb">BLAST database from your history</option>
               <option value="file">FASTA file from your history (see warning note below)</option>
             </param>
@@ -132,7 +136,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
@@ -144,9 +148,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">blastn</requirement>
-    </requirements>
     <help>
     
 .. class:: warningmark