diff tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 13:623f727cdff1 draft

Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.

--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Jan 21 13:37:01 2014 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri Mar 14 07:40:46 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.22">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.00">
     <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" merge_outputs="output1"></parallelism>
@@ -36,14 +36,16 @@
         <expand macro="input_conditional_nucleotide_db" />
 
         <param name="blast_type" type="select" display="radio" label="Type of BLAST">
-            <option value="megablast">megablast</option>
-            <option value="blastn">blastn</option>
-            <option value="blastn-short">blastn-short</option>
-            <option value="dc-megablast">dc-megablast</option>
+            <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>
+            <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
             <!-- Using BLAST 2.2.24+ this gives an error:
             BLAST engine error: Program type 'vecscreen' not supported
             <option value="vecscreen">vecscreen</option>
+            In any case, vecscreen has gone in BLAST+ 2.2.28
             -->
+            <!-- BLAST+ 2.2.28 also offers rmblastn -->
         </param>
         <expand macro="input_evalue" />
         <expand macro="input_out_format" />
@@ -63,7 +65,7 @@
         </expand>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} $query.name vs @ON_DB_SUBJECT@">
+        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
             <expand macro="output_change_format" />
         </data>
     </outputs>
@@ -74,10 +76,32 @@
             <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
             <param name="database" value="" />
             <param name="evalue_cutoff" value="1e-40" />
+            <param name="out_format" value="5" />
+            <param name="adv_opts_selector" value="basic" />
+            <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" />
+        </test>
+        <test>
+            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-40" />
             <param name="out_format" value="6" />
             <param name="adv_opts_selector" value="basic" />
             <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-40" />
+            <param name="out_format" value="cols" />
+            <param name="std_cols" value="qseqid,sseqid,pident" />
+            <param name="ext_cols" value="qlen,slen" />
+            <param name="adv_opts_selector" value="basic" />
+            <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" />
+        </test>
     </tests>
     <help>