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changeset 39:5dd84f7ab575 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 022191902de1bae6ac6570b33284287c4854ae76-dirty
author peterjc
date Tue, 23 Oct 2018 12:59:33 -0400
parents 2be8f8cc13de
children fe0c28b3673e
files test-data/rhodopsin_nucs.blastdbcmd.txt tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
diffstat 2 files changed, 23 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rhodopsin_nucs.blastdbcmd.txt	Tue Oct 23 12:59:33 2018 -0400
@@ -0,0 +1,7 @@
+gi|57163782|ref|NM_001009242.1|
+gi|2734705|gb|U59921.1|BBU59921 "1 -" +
+gi|283855845|gb|GQ290303.1| 1-4301 +
+gi|283855822|gb|GQ290312.1| "1-983"
+gi|18148870|dbj|AB062417.1| "1 -" +
+gi|12583664|dbj|AB043817.1| "1--"
+
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Oct 23 10:40:59 2018 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Oct 23 12:59:33 2018 -0400
@@ -55,7 +55,7 @@
               <option value="prompt">User entered</option>
             </param>
             <when value="file">
-                <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/>
+                <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line, optionally with space separated range, strand, and algorithm."/>
             </when>
             <when value="prompt">
                 <param name="entries" argument="-entry" type="text" optional="false" area="true" size="10x30" label="Sequence identifier(s)" help="Comma or new line separated list"/>
@@ -88,6 +88,15 @@
             <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
         </test>
         <test>
+            <!-- This uses various start end frame combinations but all recover full sequence -->
+            <param name="db_opts|db_type" value="nucl" />
+            <param name="db_opts|database" value="rhodopsin_nucs" />
+            <param name="id_opts|id_type" value="file" />
+            <param name="id_opts|entries" value="rhodopsin_nucs.blastdbcmd.txt" ftype="txt" />
+            <param name="outfmt" value="original" />
+            <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
+        </test>
+        <test>
             <param name="db_opts|db_type" value="nucl" />
             <param name="db_opts|database" value="rhodopsin_nucs" />
             <param name="id_opts|id_type" value="prompt" />
@@ -111,6 +120,12 @@
 Extracts FASTA formatted sequences from a BLAST database
 using the NCBI BLAST+ blastdbcmd command line tool.
 
+When giving a text file of entries, use one line per sequence.
+Optional valies should be space separate - the simplest syntax
+is ``identifier start-end`` (where ``end`` can be just ``-``),
+or ``identifier start-end strand`` (wheere the strand given as
+either ``+`` or ``-``).
+
 .. class:: warningmark
 
 **BLAST assigned identifiers**