diff tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @ 23:31e517610e1f draft

v0.3.0 Updated for NCBI BLAST+ 2.7.1

--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Sat Jun 30 17:22:46 2018 -0400
@@ -17,14 +17,15 @@
 @BLAST_OUTPUT@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
--db_gencode $adv_opts.db_gencode
-$adv_opts.strand
--matrix $adv_opts.matrix
-@ADV_FILTER_QUERY@
-@ADV_MAX_HITS@
-@ADV_WORD_SIZE@
-@ADV_ID_LIST_FILTER@
-@ADV_QCOV_HSP_PERC@
+    -db_gencode $adv_opts.db_gencode
+    $adv_opts.strand
+    @ADV_MATRIX@
+    @ADV_FILTER_QUERY@
+    @ADV_MAX_HITS@
+    @ADV_WORD_SIZE@
+    @ADV_ID_LIST_FILTER@
+    @ADV_QCOV_HSP_PERC@
+    @ADV_THRESHOLD@
 ## End of advanced options:
 #end if
     </command>
@@ -49,6 +50,7 @@
             <expand macro="input_parse_deflines" />
             <expand macro="advanced_optional_id_files" />
             <expand macro="input_qcov_hsp_perc" />
+            <expand macro="input_threshold" />
         </expand>
     </inputs>
     <outputs>
@@ -85,6 +87,10 @@
 
 -------
 
+@CLI_OPTIONS@
+
+-------
+
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please