diff tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.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/ncbi_blastdbcmd_wrapper.xml	Mon Sep 23 06:14:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Thu Dec 05 06:55:59 2013 -0500
@@ -1,10 +1,10 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.22">
     <description>Extract sequence(s) from BLAST database</description>
-    <requirements>
-        <requirement type="binary">blastdbcmd</requirement>
-        <requirement type="package" version="2.2.26+">blast+</requirement>
-    </requirements>
-    <version_command>blastdbcmd -version</version_command>
+    <macros>
+        <token name="@BINARY@">blastdbcmd</token>
+        <import>ncbi_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -47,39 +47,9 @@
 | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
 #end if
     </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>
+    <expand macro="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>
+        <expand macro="input_conditional_choose_db_type" />
         <conditional name="id_opts">
             <param name="id_type" type="select" label="Type of identifier list">
               <option value="file">From file</option>
@@ -132,17 +102,6 @@
 If you use this Galaxy tool in work leading to a scientific publication please
 cite the following papers:
 
-Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
-Galaxy tools and workflows for sequence analysis with applications
-in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
-
-Christiam Camacho et al. (2009).
-BLAST+: architecture and applications.
-BMC Bioinformatics. 15;10:421.
-http://dx.doi.org/10.1186/1471-2105-10-421
-
-This wrapper is available to install into other Galaxy Instances via the Galaxy
-Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
+@REFERENCES@
     </help>
 </tool>