diff tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @ 22:6f386c5dc4fb draft

v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates

--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -6,34 +6,34 @@
     </macros>
     <expand macro="parallelism" />
     <expand macro="preamble" />
-    <command>
+    <command detect_errors="aggressive">
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 blastp
--query "$query"
+-query '$query'
 @BLAST_DB_SUBJECT@
 -task $blast_type
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
--matrix $adv_opts.matrix
-@ADV_FILTER_QUERY@
-@ADV_MAX_HITS@
-@ADV_WORD_SIZE@
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-@ADV_ID_LIST_FILTER@
-@ADV_QCOV_HSP_PERC@
-## End of advanced options:
+    -matrix $adv_opts.matrix
+    @ADV_FILTER_QUERY@
+    @ADV_MAX_HITS@
+    @ADV_WORD_SIZE@
+    ##Ungapped disabled for now - see comments below
+    ##$adv_opts.ungapped
+    @ADV_ID_LIST_FILTER@
+    @ADV_QCOV_HSP_PERC@
+    $adv_opts.use_sw_tback
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/>
 
         <expand macro="input_conditional_protein_db" />
 
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
+        <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
             <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option>
             <option value="blastp-fast">blastp-fast - Use longer words for seeding, faster but less accurate</option>
             <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option>
@@ -50,11 +50,12 @@
             Can't use '-ungapped' on its own, error back is:
             Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
             Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
-            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
+            <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
             -->
             <expand macro="input_parse_deflines" />
             <expand macro="advanced_optional_id_files" />
             <expand macro="input_qcov_hsp_perc" />
+            <param argument="-use_sw_tback" type="boolean" truevalue="-use_sw_tback" falsevalue="" label="Compute locally optimal Smith-Waterman alignments" />
         </expand>
     </inputs>
     <outputs>
@@ -72,11 +73,11 @@
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="5" />
             <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
+            <param name="filter_query" value="false" />
             <param name="matrix" value="BLOSUM62" />
             <param name="max_hits" value="0" />
             <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
+            <param name="parse_deflines" value="true" />
             <param name="qcov_hsp_perc" value="25" />
             <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
         </test>
@@ -89,11 +90,11 @@
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="6" />
             <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
+            <param name="filter_query" value="false" />
             <param name="matrix" value="BLOSUM62" />
             <param name="max_hits" value="0" />
             <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
+            <param name="parse_deflines" value="true" />
             <param name="qcov_hsp_perc" value="25" />
             <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
         </test>
@@ -106,11 +107,11 @@
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="ext" />
             <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
+            <param name="filter_query" value="false" />
             <param name="matrix" value="BLOSUM62" />
             <param name="max_hits" value="0" />
             <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
+            <param name="parse_deflines" value="true" />
             <param name="qcov_hsp_perc" value="25" />
             <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
         </test>
@@ -127,7 +128,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**
@@ -150,5 +151,5 @@
 
 @REFERENCES@
     </help>
-    <expand macro="blast_citations" />    
+    <expand macro="blast_citations" />
 </tool>