# HG changeset patch
# User peterjc
# Date 1505476342 14400
# Node ID 9e483194ebf659799bae74d31bfb2745bd0de42a
# Parent  b98c41537d0fd0eade5f7f514efc8c9dca2b83c3
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit befaf16290a437209109c06c20d0deb170925d16-dirty

diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Fri Sep 15 07:52:22 2017 -0400
@@ -244,6 +244,9 @@
           (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
 ======= ======================================================================
 
 
@@ -280,7 +283,7 @@
 
     $ planemo shed_upload --tar_only tools/ncbi_blast_plus/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/blastdb.loc
     ...
     tools/ncbi_blast_plus/tool_dependencies.xml
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -55,10 +55,10 @@
               <option value="prompt">User entered</option>
             </param>
             <when value="file">
-                <param name="entries" 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 (i.e. single column tabular file)"/>
             </when>
             <when value="prompt">
-                <param name="entries" type="text" label="Sequence identifier(s)" help="Comma or new line separated list." optional="false" area="true" size="10x30"/>
+                <param name="entries" argument="-entry" type="text" optional="false" area="true" size="10x30" label="Sequence identifier(s)" help="Comma or new line separated list"/>
             </when>
         </conditional>
         <param name="outfmt" type="select" label="Output format">
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -31,9 +31,9 @@
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
         <expand macro="input_conditional_nucleotide_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="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
             <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
             <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
@@ -49,16 +49,14 @@
         <expand macro="input_out_format" />
         <expand macro="advanced_options">
             <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
-            <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
+            <param name="filter_query" argument="-dust" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
             <expand macro="input_strand" />
             <expand macro="input_max_hits" />
-            <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" />
-            
+            <param name="identity_cutoff" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" help="Use zero for no cutoff" />
+
             <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
-            <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
-                <validator type="in_range" min="0" />
-            </param>
-            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
+            <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4" />
+            <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
             <expand macro="input_parse_deflines" />
             <expand macro="advanced_optional_id_files" />
             <expand macro="input_qcov_hsp_perc" />
@@ -134,6 +132,15 @@
             <param name="out_format" value="6" />
             <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="query" value="chimera.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="db" />
+            <param name="database" value="rhodopsin_nucs" />
+            <param name="out_format" value="6" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="max_hsps" value="1" />
+            <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" />
+        </test>
         <!-- next test is passing in two blast databases -->
         <test>
             <param name="query" value="chimera.fasta" ftype="fasta" />
@@ -144,7 +151,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -17,23 +17,23 @@
 @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>
@@ -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>
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -30,11 +30,11 @@
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
 
         <expand macro="input_conditional_protein_db" />
         <expand macro="input_query_gencode" />
-        <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="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option>
             <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</option>
         </param>
@@ -48,7 +48,7 @@
             <expand macro="input_scoring_matrix" />
             <expand macro="input_max_hits" />
             <expand macro="input_word_size" />
-            <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
+            <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
             <expand macro="input_parse_deflines" />
             <expand macro="advanced_optional_id_files" />
             <expand macro="input_qcov_hsp_perc" />
@@ -107,7 +107,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -17,22 +17,22 @@
 -outfmt $outformat
     </command>
     <inputs>
-        <param name="infile" type="data" format="fasta" label="masked FASTA file"/> 
-        <param name="masking_algorithm" type="select" label="Used masking algorithm">
+        <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/>
+        <param argument="-masking_algorithm" type="select" label="Used masking algorithm">
             <option value="dust">DUST</option>
             <option value="seg" selected="true">SEG</option>
             <option value="windowmasker">windowmasker</option>
             <option value="repeat">repeat</option>
             <option value="other">other</option>
         </param>
-        <param name="masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" 
-            help ="free text to describe the options used to create the masking files. (-masking_options)">
+        <param argument="-masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input"
+            help ="Free text to describe the options used to create the masking files">
             <sanitizer invalid_char="">
                 <valid initial="string.printable" />
             </sanitizer>
         </param>
-        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" />
-        <param name="outformat" type="select" label="Output format">
+        <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" />
+        <param name="outformat" argument="-outfmt" type="select" label="Output format">
             <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>
             <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option>
             <option value="maskinfo_xml">maskinfo_xml</option>
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -22,10 +22,10 @@
     </command>
     <inputs>
         <expand macro="input_conditional_nucleotide_db" />
-        <param name="window" type="integer" value="64" label="DUST window length" />
-        <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" />
-        <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" />
-        <param name="outformat" type="select" label="Output format">
+        <param argument="-window" type="integer" value="64" label="DUST window length" />
+        <param argument="-level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" />
+        <param argument="-linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" />
+        <param name="outformat" argument="-outfmt" type="select" label="Output format">
             <!-- seqloc_* formats are not very useful
                  and what BLAST+ calls 'interval' is not what Galaxy calls interval format
             -->
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -23,7 +23,7 @@
     </xml>
     <xml name="input_out_format">
         <conditional name="output">
-            <param name="out_format" type="select" label="Output format">
+            <param name="out_format" argument="-outfmt" type="select" label="Output format">
                 <option value="6">Tabular (standard 12 columns)</option>
                 <option value="ext" selected="true">Tabular (extended 25 columns)</option>
                 <option value="cols">Tabular (select which columns)</option>
@@ -109,11 +109,11 @@
         </conditional>
     </xml>
     <xml name="input_scoring_matrix">
-        <param name="matrix" type="select" label="Scoring matrix">
+        <param argument="-matrix" type="select" label="Scoring matrix">
             <option value="BLOSUM90">BLOSUM90</option>
             <option value="BLOSUM80">BLOSUM80</option>
             <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-            <option value="BLOSUM50">BLOSUM50</option> 
+            <option value="BLOSUM50">BLOSUM50</option>
             <option value="BLOSUM45">BLOSUM45</option>
             <option value="PAM250">PAM250</option>
             <option value="PAM70">PAM70</option>
@@ -121,7 +121,7 @@
         </param>
     </xml>
     <xml name="input_query_gencode">
-        <param name="query_gencode" type="select" label="Query genetic code">
+        <param argument="-query_gencode" type="select" label="Query genetic code">
             <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
             <option value="1" selected="true">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
@@ -144,7 +144,7 @@
         </param>
     </xml>
     <xml name="input_db_gencode">
-        <param name="db_gencode" type="select" label="Database/subject genetic code">
+        <param argument="-db_gencode" type="select" label="Database/subject genetic code">
             <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
             <option value="1" selected="true">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
@@ -178,7 +178,7 @@
                     <options from_data_table="blastdb" />
                 </param>
                 <param name="histdb" type="hidden" value="" />
-                <param name="subject" type="hidden" value="" /> 
+                <param name="subject" type="hidden" value="" />
             </when>
             <when value="histdb">
                 <param name="database" type="hidden" value="" />
@@ -188,7 +188,7 @@
             <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 name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
             </when>
         </conditional>
     </xml>
@@ -214,7 +214,7 @@
             <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 name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
             </when>
         </conditional>
     </xml>
@@ -257,36 +257,33 @@
         </conditional>
     </xml>
     <xml name="input_parse_deflines">
-        <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
+        <param argument="-parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
     </xml>
     <xml name="input_filter_query_default_false">
-        <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
+        <param name="filter_query" argument="-seg" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
     </xml>
     <xml name="input_filter_query_default_true">
-        <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
+        <param name="filter_query" argument="-seg" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
     </xml>
     <xml name="input_max_hits">
-        <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-            <validator type="in_range" min="0" />
-        </param>        
+        <param name="max_hits" type="integer" min="0" value="0" label="Maximum hits to show" help="Use zero for default limits" />
+        <param argument="-max_hsps" type="integer" min="1" optional="true" value="" label="Maximum number of HSPs (alignments) to keep for any single query-subject pair" help="The HSPs shown will be the best as judged by expect value. If this option is not set, BLAST shows all HSPs meeting the expect value criteria" />
     </xml>
     <xml name="input_evalue">
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
+        <param name="evalue_cutoff" argument="-evalue" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
     </xml>
     <xml name="input_word_size">
-        <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-            <validator type="in_range" min="0" />
-        </param>        
+        <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2" />
     </xml>
     <xml name="input_strand">
-        <param name="strand" type="select" label="Query strand(s) to search against database/subject">
+        <param argument="-strand" type="select" label="Query strand(s) to search against database/subject">
             <option value="-strand both">Both</option>
             <option value="-strand plus">Plus (forward)</option>
             <option value="-strand minus">Minus (reverse complement)</option>
         </param>
     </xml>
     <xml name="input_qcov_hsp_perc">
-        <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qcovhsp"/>
+        <param argument="-qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qcovhsp"/>
     </xml>
     <xml name="advanced_options">
         <conditional name="adv_opts">
@@ -312,15 +309,15 @@
             </param>
             <when value="none" />
             <when value="gilist">
-                <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file"
+                <param argument="-gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file"
                        help="This option is only available for database searches."/>
             </when>
             <when value="negative_gilist">
-                <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file"
+                <param argument="-negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file"
                        help="This option is only available for database searches."/>
             </when>
             <when value="seqidlist">
-                <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's"
+                <param argument="-seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's"
                        help="This option is only available for database searches."/>
             </when>
         </conditional>
@@ -369,13 +366,16 @@
 ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments
 ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI)
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
-#if str($output.out_format) in ["6", "ext", "cols", "5"]:
-## Most output formats use this, including tabular and XML:
--max_target_seqs $adv_opts.max_hits
-#else
-## Text and HTML output formats 0-4 currently need this instead:
--num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits
+    #if str($output.out_format) in ["6", "ext", "cols", "5"]:
+        ## Most output formats use this, including tabular and XML:
+        -max_target_seqs $adv_opts.max_hits
+    #else
+        ## Text and HTML output formats 0-4 currently need this instead:
+        -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits
+    #end if
 #end if
+#if str($adv_opts.max_hsps)
+    -max_hsps $adv_opts.max_hsps
 #end if
     </token>
     <token name="@ADV_WORD_SIZE@">
@@ -483,7 +483,7 @@
     <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark
 
 **Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
+For large input datasets it is advisable to allow overnight processing.
 
 -----
     </token>
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -49,7 +49,7 @@
 &gt; "$outfile"
     </command>
     <inputs>
-        <param name="dbtype" type="select" display="radio" label="Molecule type of input">
+        <param argument="-dbtype" type="select" display="radio" label="Molecule type of input">
             <option value="prot">protein</option>
             <option value="nucl">nucleotide</option>
         </param>
@@ -57,13 +57,13 @@
              NOTE Double check the new database would be self contained first
         -->
         <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->
-        <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />
-        <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />
-        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="false" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" />
-        <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />
+        <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />
+        <param argument="-title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />
+        <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="false" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" />
+        <param argument="-hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />
         <!-- SEQUENCE MASKING OPTIONS -->
         <!-- Note this is an optional parameter - default should be NO files -->
-        <param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" />
+        <param name="mask_data_file" argument="-mask_data" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" />
         <!-- TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? -->
         <!-- TAXONOMY OPTIONS -->
         <conditional name="tax">
@@ -77,11 +77,11 @@
             <when value="">
             </when>
             <when value="id">
-                <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" help="Integer &gt;=0, e.g. 9606 for Homo sapiens" min="0" />
+                <param argument="-taxid" type="integer" min="0" value="" label="NCBI taxonomy ID" help="Integer &gt;=0, e.g. 9606 for Homo sapiens" />
             </when>
             <!-- TODO: File format?
             <when value="map">
-                <param name="taxmap" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />
+                <param name="taxmap" argument="-taxid_map" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" />
             </when>
             -->
         </conditional>
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_makeprofiledb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -10,7 +10,7 @@
 mkdir -p $outfile.files_path &amp;&amp;
 makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}'
 
-##We turn $infile_list into $infiles with a configfile entry defined below
+##We turn $input_file into $infiles with a configfile entry defined below
 -in '$infiles'
 
 #if $title:
@@ -42,13 +42,12 @@
         </configfile>
     </configfiles>
     <inputs>
-        <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1"
+        <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="pssm-asn1"
                label="Input PSSM files(s)"
                help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" />
-        <param name="infile_list" type="data" multiple="true" format="pssm-asn1" />
 
-        <param name="title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" />
-        <param name="threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" />
+        <param argument="-title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" />
+        <param argument="-threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" />
 
         <!-- output options -->
         <!-- Initially we're only offering the default, RPS databases for use with rpsblast and rpstblastn
@@ -66,19 +65,19 @@
             </param>
             <when value="yes" />
             <when value="no">
-                <param name="gapopen" type="integer" size="5" value="" label="Cost to open a gap" />
-                <param name="gapextend" type="integer" size="5" value="" label="Cost to extend a gap" />
-                <param name="scale" type="float" size="5" value="" label="PSSM scale factor" />
+                <param argument="-gapopen" type="integer" size="5" value="" label="Cost to open a gap" />
+                <param argument="-gapextend" type="integer" size="5" value="" label="Cost to extend a gap" />
+                <param argument="-scale" type="float" size="5" value="" label="PSSM scale factor" />
                 <expand macro="input_scoring_matrix" />
             </when>
         </conditional>
 
         <!--  Delta Blast Options -->
-        <param name="exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true" 
+        <param argument="-exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true"
             label="Exclude invalid domains?"
             help="Exclude domains that do not pass validation test" />
-        <param name="obsr_threshold" type="float" size="5" value="6.0"
-            label="Observation threshold"            
+        <param argument="-obsr_threshold" type="float" size="5" value="6.0"
+            label="Observation threshold"
             help="Exclude domains with with maximum number of independent observations below this threshold" />
     </inputs>
     <outputs>
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -27,7 +27,7 @@
 #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_pssm" />
 
@@ -61,7 +61,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**
@@ -76,7 +76,7 @@
 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
 
 *Kog* - PSSMs from automatically aligned sequences and sequence
-fragments classified in the KOGs resource, the eukaryotic 
+fragments classified in the KOGs resource, the eukaryotic
 counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/
 
 *Cog* - PSSMs from automatically aligned sequences and sequence
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -28,7 +28,7 @@
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
 
         <expand macro="input_conditional_pssm" />
 
@@ -61,7 +61,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**
@@ -76,7 +76,7 @@
 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
 
 *Kog* - PSSMs from automatically aligned sequences and sequence
-fragments classified in the KOGs resource, the eukaryotic 
+fragments classified in the KOGs resource, the eukaryotic
 counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/
 
 *Cog* - PSSMs from automatically aligned sequences and sequence
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -30,10 +30,10 @@
 #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_nucleotide_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="tblastn">tblastn - Traditional TBLASTN to compare protein query to translated nucleotide database</option>
             <option value="tblastn-fast">tblastn-fast - Use longer words for seeding, faster but less accurate</option>
         </param>
@@ -51,7 +51,7 @@
             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 tblastn 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" />
@@ -144,7 +144,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**
diff -r b98c41537d0f -r 9e483194ebf6 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri May 19 06:04:55 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri Sep 15 07:52:22 2017 -0400
@@ -29,7 +29,7 @@
 #end if
     </command>
     <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+        <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
 
         <expand macro="input_conditional_nucleotide_db" />
         <expand macro="input_query_gencode" />
@@ -69,7 +69,7 @@
         </test>
     </tests>
     <help>
-    
+
 @SEARCH_TIME_WARNING@
 
 **What it does**