diff tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 15:c16c30e9ad5b draft

Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)

--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon Dec 01 05:59:16 2014 -0500
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Sun Jul 05 10:37:27 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.01">
+<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.03">
     <description>Search protein domain database (PSSMs) with protein query sequence(s)</description>
     <!-- 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" />
@@ -6,7 +6,7 @@
         <token name="@BINARY@">deltablast</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <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
@@ -15,19 +15,18 @@
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #end if
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
 
@@ -41,8 +40,8 @@
             <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
             <expand macro="input_filter_query_default_false" />
             <expand macro="input_max_hits" />
-            <expand macro="input_word_size" />
             <expand macro="input_parse_deflines" />
+            <expand macro="input_qcov_hsp_perc" />
         </expand>
     </inputs>
     <outputs>
@@ -52,6 +51,19 @@
 
         </data>
     </outputs>
+    <tests>
+        <!-- Disable for ToolShed where *.loc tests not yet supported
+             See https://github.com/peterjc/galaxy_blast/issues/53
+        <test>
+            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="db" />
+            <param name="database" value="cd00003_and_cd00008" />
+            <param name="evalue_cutoff" value="1e-8" />
+            <param name="out_format" value="6" />
+            <output name="output1" file="empty_file.dat" ftype="tabular" />
+        </test>
+        -->
+    </tests>
     <help>
     
 @SEARCH_TIME_WARNING@