diff tools/ncbi_blast_plus/ncbi_macros.xml @ 27:6f8ea4b9a2c4 draft

"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"

--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Sat Jul 20 18:36:36 2019 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Wed Sep 09 15:32:17 2020 +0000
@@ -1,5 +1,7 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">0.3.3</token>
+    <token name="@TOOL_VERSION@">2.7.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">16.10</token>
     <xml name="parallelism">
         <!-- 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" />
@@ -7,7 +9,7 @@
 
     <xml name="preamble">
         <requirements>
-            <requirement type="package" version="2.7.1">blast</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">blast</requirement>
         </requirements>
         <version_command>@BINARY@ -version</version_command>
     </xml>
@@ -426,14 +428,40 @@
               <option value="prot">Protein</option>
             </param>
             <when value="nucl">
-                <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database">
-                    <options from_data_table="blastdb" />
-                </param>
+                <conditional name="db_origin">
+                    <param name="db_origin_selector" type="select" label="Subject database/sequences">
+                          <option value="db" selected="true">Locally installed BLAST database</option>
+                          <option value="histdb">BLAST database from your history</option>
+                    </param>
+                    <when value="db">
+                        <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database">
+                            <options from_data_table="blastdb" />
+                        </param>
+                        <param name="histdb" type="hidden" value="" />
+                    </when>
+                    <when value="histdb">
+                        <param name="database" type="hidden" value="" />
+                        <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />
+                    </when>
+                </conditional>
             </when>
             <when value="prot">
-                <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database">
-                    <options from_data_table="blastdb_p" />
-                </param>
+                <conditional name="db_origin">
+                    <param name="db_origin_selector" type="select" label="Subject database/sequences">
+                          <option value="db" selected="true">Locally installed BLAST database</option>
+                          <option value="histdb">BLAST database from your history</option>
+                      </param>
+                      <when value="db">
+                          <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database">
+                            <options from_data_table="blastdb_p" />
+                        </param>
+                        <param name="histdb" type="hidden" value="" />
+                      </when>
+                      <when value="histdb">
+                        <param name="database" type="hidden" value="" />
+                        <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />
+                      </when>
+                </conditional>
             </when>
         </conditional>
     </xml>
@@ -574,6 +602,17 @@
 #end if
     ]]></token>
 
+    <!-- Implement -dbtype and -db command line options (in blastdbcmd) -->
+    <token name="@DBCMD_OPTS@"><![CDATA[
+-dbtype "$db_opts.db_type"
+#if $db_opts.db_origin.db_origin_selector=="db":
+  -db "${db_opts.db_origin.database.fields.path.replace(',',' ')}"
+#else if $db_opts.db_origin.db_origin_selector=="histdb":
+  -db '${os.path.join($db_opts.db_origin.histdb.extra_files_path, "blastdb")}'
+#end if
+    ]]></token>
+
+    <!-- Implement -db ... / -subject ... command line options -->
     <token name="@BLAST_DB_SUBJECT@"><![CDATA[
 #if $db_opts.db_opts_selector == "db":
   -db '${" ".join(str($db_opts.database.fields.path).split(","))}'
@@ -699,6 +738,15 @@
 #end if
 ]]></token>
 
+    <!-- @ON_DBCMD_OPTS@ is for use with @DBCMD_OPTS@ -->
+    <token name="@ON_DBCMD_OPTS@"><![CDATA[
+#if str($db_opts.db_origin.db_origin_selector)=="db"
+'${db_opts.db_origin.database}'
+#else
+'${db_opts.db_origin.histdb.name}'
+#end if
+]]></token>
+
     <token name="@REFERENCES@"><![CDATA[
 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
 NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39