# HG changeset patch
# User peterjc
# Date 1505484176 14400
# Node ID 3b4efe26da79cd9a82c25986ce0be0f1c1184b45
# Parent  9e483194ebf659799bae74d31bfb2745bd0de42a
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit dc88568c900086550ce206dd83bad65e991df743-dirty

diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Fri Sep 15 07:52:22 2017 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Fri Sep 15 10:02:56 2017 -0400
@@ -244,9 +244,10 @@
           (internal change only).
 v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
-        - Show the BLAST option corresponding to each tool parameter
-        - Add ``-max_hsps`` option
-        - Add ``-use_sw_tback`` option for BLASTP
+        - Show BLAST command line argument corresponding to each tool
+          parameter (contribution from Nicola Soranzo).
+        - Add ``-max_hsps`` option (contribution from Nicola Soranzo).
+        - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo).
 ======= ======================================================================
 
 
diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri Sep 15 07:52:22 2017 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri Sep 15 10:02:56 2017 -0400
@@ -134,7 +134,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri Sep 15 07:52:22 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri Sep 15 10:02:56 2017 -0400
@@ -32,7 +32,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info
diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri Sep 15 10:02:56 2017 -0400
@@ -105,7 +105,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 Extracts FASTA formatted sequences from a BLAST database
@@ -138,5 +138,5 @@
 
 @REFERENCES@
     </help>
-    <expand macro="blast_citations" />    
+    <expand macro="blast_citations" />
 </tool>
diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Sep 15 07:52:22 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Sep 15 10:02:56 2017 -0400
@@ -174,7 +174,7 @@
               <option value="file">FASTA file from your history (see warning note below)</option>
             </param>
             <when value="db">
-                <param name="database" type="select" multiple="true" label="Nucleotide BLAST database">
+                <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="" />
@@ -182,13 +182,13 @@
             </when>
             <when value="histdb">
                 <param name="database" type="hidden" value="" />
-                <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />
+                <param name="histdb" argument="-db" type="data" format="blastdbn" label="Nucleotide BLAST database" />
                 <param name="subject" type="hidden" value="" />
             </when>
             <when value="file">
                 <param name="database" type="hidden" value="" />
                 <param name="histdb" type="hidden" value="" />
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
+                <param argument="subject" type="data" format="fasta" label="Nucleotide FASTA subject file to use instead of a database"/>
             </when>
         </conditional>
     </xml>
@@ -200,7 +200,7 @@
               <option value="file">FASTA file from your history (see warning note below)</option>
             </param>
             <when value="db">
-                <param name="database" type="select" multiple="true" label="Protein BLAST database">
+                <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="" />
@@ -208,13 +208,13 @@
             </when>
             <when value="histdb">
                 <param name="database" type="hidden" value="" />
-                <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />
+                <param name="histdb" argument="db" type="data" format="blastdbp" label="Protein BLAST database" />
                 <param name="subject" type="hidden" value="" />
             </when>
             <when value="file">
                 <param name="database" type="hidden" value="" />
                 <param name="histdb" type="hidden" value="" />
-                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
+                <param argument="subject" type="data" format="fasta" label="Protein FASTA subject file to use instead of a database"/>
             </when>
         </conditional>
     </xml>