diff tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 11:4c4a0da938ff draft

Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. Supports $GALAXY_SLOTS. Includes more tests and heavy use of macros.

--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Mon Sep 23 06:14:13 2013 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Thu Dec 05 06:55:59 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.11">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.22">
     <description>Convert BLAST XML output to tabular</description>
     <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
     <command interpreter="python">
@@ -17,7 +17,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
+        <data name="tabular_file" format="tabular" label="$blastxml_file.display_name (as tabular)" />
     </outputs>
     <requirements>
     </requirements>
@@ -70,6 +70,16 @@
             <!-- Note this has some white space differences from the actual blastp output -->
             <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" />
+            <param name="out_format" value="ext" />
+            <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" />
+        </test>
     </tests>
     <help>
     
@@ -104,13 +114,13 @@
 but this takes longer to calculate. Most (but not all) of these columns are
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 22 column tabular
-BLAST output. This tool now uses this extended 24 column output by default.
+workflow filtering steps that accept either the 12 or 25 column tabular
+BLAST output. This tool now uses this extended 25 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
 ------ ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
+    13 sallseqid     All subject Seq-id(s), separated by ';'
     14 score         Raw score
     15 nident        Number of identical matches
     16 positive      Number of positive-scoring matches
@@ -122,6 +132,7 @@
     22 sseq          Aligned part of subject sequence
     23 qlen          Query sequence length
     24 slen          Subject sequence length
+    25 salltitles    All subject title(s), separated by '&lt;&gt;'
 ====== ============= ===========================================
 
 Beware that the XML file (and thus the conversion) and the tabular output