diff tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml @ 5:393a7a35383c draft

Uploaded v0.0.14 adding local BLAST database support. This *requires* the matching update to the blast_datatypes repository. This adds basic wrappers for makeblastdb and blastdbinfo. This update includes work by Edward Kirton.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri Nov 09 06:53:55 2012 -0500
@@ -0,0 +1,63 @@
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.2">
+    <description>Show BLAST database information from blastdbcmd</description>
+    <command>
+blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out $info
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+	<!-- Suspect blastdbcmd sometimes fails to set error level -->
+	<regex match="Error:" />
+	<regex match="EXception:" />
+    </stdio>
+    <inputs>
+        <conditional name="db_opts">
+            <param name="db_type" type="select" label="Type of BLAST database">
+              <option value="nucl" selected="True">Nucleotide</option>
+              <option value="prot">Protein</option>
+            </param>
+            <when value="nucl">
+                <param name="database" type="select" label="Nucleotide BLAST database">
+                    <options from_file="blastdb.loc">
+                      <column name="value" index="0"/>
+                      <column name="name" index="1"/>
+                      <column name="path" index="2"/>
+                    </options>
+                </param>
+            </when>
+            <when value="prot">
+                <param name="database" type="select" label="Protein BLAST database">
+                    <options from_file="blastdb_p.loc">
+                      <column name="value" index="0"/>
+                      <column name="name" index="1"/>
+                      <column name="path" index="2"/>
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="info" format="txt" label="${db_opts.database.fields.name} info" />
+    </outputs>
+    <requirements>
+        <requirement type="binary">blastdbcmd</requirement>
+    </requirements>
+    <help>
+    
+**What it does**
+
+Calls the NCBI BLAST+ blastdbcmd command line tool with the -info
+switch to give summary information about a BLAST database, such as
+the size (number of sequences and total length) and date.
+
+-------
+
+**References**
+
+Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
+
+Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
+
+    </help>
+</tool>