--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blastxml_to_tabular.xml	Fri Aug 17 09:11:43 2012 -0400
@@ -0,0 +1,127 @@
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
+    <description>Convert BLAST XML output to tabular</description>
+    <command interpreter="python">
+      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
+    </command>
+    <inputs>
+        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
+        <param name="out_format" type="select" label="Output format">
+            <option value="std" selected="True">Tabular (standard 12 columns)</option>
+            <option value="ext">Tabular (extended 24 columns)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
+    </outputs>
+    <requirements>
+    </requirements>
+    <tests>
+        <test>
+            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar -->
+            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
+            <param name="out_format" value="ext" />
+            <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar -->
+            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <!-- Note this has some white space differences from the actual blastp output -->
+            <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <!-- Note this has some white space differences from the actual blastx output -->
+            <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
+            <param name="out_format" value="ext" />
+            <!-- Note this has some white space and XXXX masking differences from the actual blastx output -->
+            <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <!-- Note this has some white space differences from the actual blastx output -->
+            <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <!-- Note this has some white space differences from the actual blastp output -->
+            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
+            <param name="out_format" value="ext" />
+            <!-- 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>
+    </tests>
+    <help>
+    
+**What it does**
+
+NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
+formats including tabular and a more detailed XML format. A complex workflow
+may need both the XML and the tabular output - but running BLAST twice is
+slow and wasteful.
+
+This tool takes the BLAST XML output and by default converts it into the
+standard 12 column tabular equivalent:
+
+====== ========= ============================================
+Column NCBI name Description
+------ --------- --------------------------------------------
+     1 qseqid    Query Seq-id (ID of your sequence)
+     2 sseqid    Subject Seq-id (ID of the database hit)
+     3 pident    Percentage of identical matches
+     4 length    Alignment length
+     5 mismatch  Number of mismatches
+     6 gapopen   Number of gap openings
+     7 qstart    Start of alignment in query
+     8 qend      End of alignment in query
+     9 sstart    Start of alignment in subject (database hit)
+    10 send      End of alignment in subject (database hit)
+    11 evalue    Expectation value (E-value)
+    12 bitscore  Bit score
+====== ========= ============================================
+
+The BLAST+ tools can optionally output additional columns of information,
+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.
+
+====== ============= ===========================================
+Column NCBI name     Description
+------ ------------- -------------------------------------------
+    13 sallseqid     All subject Seq-id(s), separated by a ';'
+    14 score         Raw score
+    15 nident        Number of identical matches
+    16 positive      Number of positive-scoring matches
+    17 gaps          Total number of gaps
+    18 ppos          Percentage of positive-scoring matches
+    19 qframe        Query frame
+    20 sframe        Subject frame
+    21 qseq          Aligned part of query sequence
+    22 sseq          Aligned part of subject sequence
+    23 qlen          Query sequence length
+    24 slen          Subject sequence length
+====== ============= ===========================================
+
+Beware that the XML file (and thus the conversion) and the tabular output
+direct from BLAST+ may differ in the presence of XXXX masking on regions
+low complexity (columns 21 and 22), and thus also calculated figures like
+the percentage idenity (column 3).
+
+    </help>
+</tool>