--- a/diamond.xml	Tue Aug 08 16:33:49 2017 -0400
+++ b/diamond.xml	Thu Sep 27 06:30:30 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="bg_diamond" name="Diamond" version="@VERSION@.1">
+<tool id="bg_diamond" name="Diamond" version="@VERSION@.0">
     <description>alignment tool for short sequences against a protein database</description>
     <macros>
         <import>macros.xml</import>
@@ -18,26 +18,21 @@
     &&
 
     diamond
-        $method_select.method_select
+        $method_cond.method_select
         --threads "\${GALAXY_SLOTS:-12}"
         --db ./database
         --query '$query'
-        #if $method_select.method_select == "blastx"
-          --query-gencode '$query_gencode'
+        #if $method_cond.method_select == "blastx"
+          --query-gencode '$method_cond.query_gencode'
+          --strand '$method_cond.query_strand'
+	  --min-orf $method_cond.min_orf
+	  #if $method_cond.frameshift_cond.frameshift_select == 'yes'
+	          --frameshift $method_cond.frameshift_cond.frameshift
+		  $method_cond.frameshift_cond.range_culling
+          #end if
         #end if
 
-        #if $output.outfmt == "5"
-            --outfmt '5'
-            --out '$blast_xml'
-            $output.salltitles
-        #else if $output.outfmt == "6"
-            --outfmt '6' #echo ' '.join(str($output.fields).split(','))
-            --out '$blast_tabular'
-        #else if $output.outfmt == "101"
-            --outfmt '101'
-            --out '$sam_output'
-            $output.salltitles
-        #end if
+        @OUTPUT_ARGS@
 
         --compress '0'
         #if $sensitivity == "1"
@@ -46,16 +41,17 @@
           --more-sensitive
         #end if
 
-        --gapopen '$gapopen'
-        --gapextend '$gapextend'
+        #if str($gapopen) != "":
+          --gapopen '$gapopen'
+        #end if
+        #if str($gapextend) != "":
+          --gapextend '$gapextend'
+        #end if
         --matrix '$matrix'
-        --seg '$seg'
+        --comp-based-stats '$comp_based_stats'
+        --masking '$masking'
 
-        #if str($hit_filter.hit_filter_select) == 'max':
-            --max-target-seqs '$hit_filter.max_target_seqs'
-        #else:
-            --top '$hit_filter.top'
-        #end if
+        @HITFILTER_ARGS@
 
         #if str($filter_score.filter_score_select) == 'evalue':
             --evalue '$filter_score.evalue'
@@ -65,131 +61,120 @@
 
         --id '$id'
         --query-cover '$query_cover'
+        --subject-cover '$subject_cover'
         --block-size '$block_size'
+        #if str($unal) == '1':
+            --unal 1 --un '$unalqueries' 
+        #end if
+        $no_self_hits
+        #if $tax_cond.tax_select == 'file':
+            --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'`
+        #else if  $tax_cond.tax_select == 'list':
+            --taxonlist '$tax_cond.taxonlist'
+        #end if
 ]]>
     </command>
-
     <inputs>
-        <conditional name="method_select">
-          <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)">
-              <option value="blastp">Align amino acid query sequences (blastp)</option>
-              <option value="blastx">Align DNA query sequences (blastx)</option>
-          </param>
-          <when value="blastx">
-            <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
-                <option value="1">The Standard Code</option>
-                <option value="2">The Vertebrate Mitochondrial Code</option>
-                <option value="3">The Yeast Mitochondrial Code</option>
-                <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-                <option value="5">The Invertebrate Mitochondrial Code</option>
-                <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-                <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
-                <option value="10">The Euplotid Nuclear Code</option>
-                <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
-                <option value="12">The Alternative Yeast Nuclear Code</option>
-                <option value="13">The Ascidian Mitochondrial Code</option>
-                <option value="14">The Alternative Flatworm Mitochondrial Code</option>
-                <option value="16">Chlorophycean Mitochondrial Code</option>
-                <option value="21">Trematode Mitochondrial Code</option>
-                <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
-                <option value="23">Thraustochytrium Mitochondrial Code</option>
-                <option value="24">Pterobranchia Mitochondrial Code</option>
-                <option value="5">Candidate Division SR1 and Gracilibacteria Code</option>
-                <option value="26">Pachysolen tannophilus Nuclear Code</option>
+        <conditional name="method_cond">
+            <param name="method_select" type="select" label="What do you want to align?" help="(blastp/blastx)">
+                <option value="blastp">Align amino acid query sequences (blastp)</option>
+                <option value="blastx">Align DNA query sequences (blastx)</option>
             </param>
-          </when>
-          <when value="blastp">
-          </when>
+            <when value="blastx">
+                <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
+                    <option value="1">The Standard Code</option>
+                    <option value="2">The Vertebrate Mitochondrial Code</option>
+                    <option value="3">The Yeast Mitochondrial Code</option>
+                    <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
+                    <option value="5">The Invertebrate Mitochondrial Code</option>
+                    <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
+                    <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
+                    <option value="10">The Euplotid Nuclear Code</option>
+                    <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
+                    <option value="12">The Alternative Yeast Nuclear Code</option>
+                    <option value="13">The Ascidian Mitochondrial Code</option>
+                    <option value="14">The Alternative Flatworm Mitochondrial Code</option>
+                    <option value="16">Chlorophycean Mitochondrial Code</option>
+                    <option value="21">Trematode Mitochondrial Code</option>
+                    <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
+                    <option value="23">Thraustochytrium Mitochondrial Code</option>
+                    <option value="24">Pterobranchia Mitochondrial Code</option>
+                    <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
+                    <option value="26">Pachysolen tannophilus Nuclear Code</option>
+                </param>
+                <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
+    
+                <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
+                    <option value="both" selected="True">Both</option>
+                    <option value="plus">Plus</option>
+                    <option value="minus">Minus</option>
+                </param>
+                <conditional name="frameshift_cond">
+                    <param name="frameshift_select" type="select" label="Allow for frameshifts?" help="">
+                        <option value="yes">yes</option>
+                        <option value="no" selected="true">no</option>
+                    </param>
+                    <when value="yes">
+                        <param argument="--range-culling" name="range_culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode"/>
+                        <param argument="--frameshift" type="integer" value="0" label="frame shift penalty" help="Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively." />
+                    </when>
+                    <when value="no"/>
+                </conditional>
+            </when>
+            <when value="blastp">
+            </when>
         </conditional>
         <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
         <conditional name="ref_db_source">
-          <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options">
-            <option value="indexed">Use a built-in index</option>
-            <option value="history">Use one from the history</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
-              <options from_data_table="diamond_database">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>
-          <when value="history">
-            <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />
-          </when>
-        </conditional>
-        <conditional name="output">
-            <param argument="--outfmt" type="select" label="Format of output file " help="">
-                <option value="5">BLAST XML</option>
-                <option value="6">BLAST tabular</option>
-                <option value="101">SAM</option>
+            <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options">
+                <option value="indexed">Use a built-in index</option>
+                <option value="history">Use one from the history</option>
             </param>
-            <when value="5">
-                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/>
-            </when>
-            <when value="6">
-                <param name="fields" type="select" label="Tabular fields" help="" multiple="true">
-                    <option value="qseqid" selected="true">Query Seq - id</option>
-                    <option value="sseqid" selected="true">Subject Seq - id</option>
-                    <option value="sallseqid">All subject Seq - id(s)</option>
-                    <option value="qlen">Query sequence length</option>
-                    <option value="slen">Subject sequence length</option>
-                    <option value="pident" selected="true">Percentage of identical matches</option>
-                    <option value="length" selected="true">Alignment length</option>
-                    <option value="nident">Number of identical matches</option>
-                    <option value="mismatch" selected="true">Number of mismatches</option>
-                    <option value="positive">Number of positive - scoring matches</option>
-                    <option value="gapopen" selected="true">Number of gap openings</option>
-                    <option value="gaps">Total number of gaps</option>
-                    <option value="ppos">Percentage of positive - scoring matches</option>
-                    <option value="qstart" selected="true">Start of alignment in query</option>
-                    <option value="qend" selected="true">End of alignment in query</option>
-                    <option value="sstart" selected="true">Start of alignment in subject</option>
-                    <option value="send" selected="true">End of alignment in subject</option>
-                    <option value="qseq">Aligned part of query sequence</option>
-                    <option value="sseq">Aligned part of subject sequence</option>
-                    <option value="evalue" selected="true">Expect value</option>
-                    <option value="bitscore" selected="true">Bit score</option>
-                    <option value="score">Raw score</option>
-                    <option value="qframe">Query frame</option>
-                    <option value="stitle">Subject Title</option>
-                    <option value="salltitles">All Subject Title(s)</option>
-                    <option value="qcovhsp">Query Coverage Per HSP</option>
+            <when value="indexed">
+                <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
+                    <options from_data_table="diamond_database">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+                    </options>
                 </param>
             </when>
-            <when value="101">
-                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/>
+            <when value="history">
+                <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />
             </when>
         </conditional>
-        <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. More sensitivity may increase computation time">
-          <option value="0" selected="True">Default</option>
-          <option value="1">Sensitive</option>
-          <option value="2">More Sensitive</option>
+        <expand macro="output_type_macro" />
+        <param name="no_self_hits" argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true" label="suppress reporting of identical self hits?" help=""/>
+        <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. The sensitive mode is a lot more sensitive than the default and generally recommended for aligning longer sequences. The more sensitive mode provides even more sensitivity. More sensitivity may increase computation time.">
+            <option value="0" selected="True">Default</option>
+            <option value="1">Sensitive</option>
+            <option value="2">More Sensitive</option>
+        </param>
+        <param argument="--matrix" type="select" label="Scoring matrix" help="In parentheses are the supported values for (gap open)/(gap extend). In brackets are default gap penalties">
+            <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option>
+            <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option>
+            <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option>
+            <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
+            <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option>
+            <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option>
+            <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option>
+            <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
         </param>
-        <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" />
-        <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" />
-        <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)">
-            <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option>
-            <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option>
-            <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option>
-            <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option>
-            <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option>
-            <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option>
-            <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option>
-            <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option>
-        </param>
-        <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/>
-        <conditional name="hit_filter">
-            <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
-                <option value="max">Maximum number of target sequences</option>
-                <option value="top">Percentage of top alignment score</option>
+        <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="leave empty for default (see scoring matrix)" />
+        <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" />
+        <param name="comp_based_stats" argument="--comp-based-stats" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable composition based statistics?" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"/>
+        <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
+        <conditional name="tax_cond">
+            <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
+                <option value="no">No</option>
+                <option value="list">list of taxids entered manually</option>
+                <option value="file">list of taxids from single column tabular file</option>
             </param>
-            <when value="max">
-                <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to keep alignments for" help="" />
+            <when value="no"/>
+            <when value="list">
+                <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="" />
             </when>
-            <when value="top">
-                <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
+            <when value="file">
+                <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
             </when>
         </conditional>
         <conditional name="filter_score">
@@ -204,47 +189,131 @@
                 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
             </when>
         </conditional>
+        <expand macro="hit_filter_macro" />
         <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" />
         <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" />
+        <param name="subject_cover" argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="" />
         <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
+        <param argument="--unal" type="boolean" truevalue="1" falsevalue="0" checked="false" label="report unaligned queries" help=""/>
     </inputs>
-
     <outputs>
-        <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}">
-            <filter>output["outfmt"] == "5"</filter>
-        </data>
-        <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">
-            <filter>output["outfmt"] == "6"</filter>
-        </data>
-        <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
-            <filter>output["outfmt"] == "101"</filter>
+        <expand macro="output_macro" />
+        <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)">
+            <filter>unal == "1"</filter>
         </data>
     </outputs>
-
     <tests>
         <test>
-            <param name="method_select" value="blastp" />
+            <conditional name="method_cond">
+                <param name="method_select" value="blastp" />
+            </conditional>
             <param name="query" value="protein.fasta" ftype="fasta"/>
-            <param name="db_source" value="history"/>
-            <param name="reference_database" value="db.dmnd"/>
-            <param name="outfmt" value="6"/>
-            <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
+            <conditional name="ref_db_source">
+                <param name="db_source" value="history"/>
+                <param name="reference_database" value="db.dmnd"/>
+            </conditional>
+            <conditional name="output">
+                <param name="outfmt" value="6"/>
+                <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
+            </conditional>
             <param name="sensitivity" value="0"/>
-            <param name="gapopen" value="11"/>
-            <param name="gapextend" value="1"/>
             <param name="matrix" value="BLOSUM62"/>
-            <param name="seg" value="yes"/>
-            <param name="hit_filter_select" value="max"/>
-            <param name="max_target_seqs" value="25" />
-            <param name="filter_score_select" value="evalue"/>
-            <param name="evalue" value="0.001" />
+            <param name="comp-based-stat" value="1"/>
+            <param name="masking" value="1"/>
+            <conditional name="hit_filter">
+                <param name="hit_filter_select" value="max"/>
+                <param name="max_target_seqs" value="25" />
+            </conditional>
+            <conditional name="filter_score">
+                <param name="filter_score_select" value="evalue"/>
+                <param name="evalue" value="0.001" />
+            </conditional>
             <param name="id" value="0"/>
             <param name="query_cover" value="0"/>
             <param name="block_size" value="2"/>
             <output name="blast_tabular" file="diamond_results.tabular"/>
         </test>
+        <test>
+            <conditional name="method_cond">
+                <param name="method_select" value="blastp" />
+            </conditional>
+            <param name="query" value="protein.fasta" ftype="fasta"/>
+            <conditional name="ref_db_source">
+                <param name="db_source" value="history"/>
+                <param name="reference_database" value="db-wtax.dmnd"/>
+            </conditional>
+            <conditional name="tax_cond">
+		    <param name="tax_select" value="list"/>
+                    <param name="taxonlist" value="2" />
+            </conditional>
+            <conditional name="output">
+                <param name="outfmt" value="6"/>
+                <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
+            </conditional>
+            <param name="sensitivity" value="0"/>
+            <param name="matrix" value="BLOSUM62"/>
+            <param name="comp-based-stat" value="1"/>
+            <param name="masking" value="1"/>
+            <conditional name="hit_filter">
+                <param name="hit_filter_select" value="max"/>
+                <param name="max_target_seqs" value="25" />
+            </conditional>
+            <conditional name="filter_score">
+                <param name="filter_score_select" value="evalue"/>
+                <param name="evalue" value="0.001" />
+            </conditional>
+            <param name="id" value="0"/>
+            <param name="query_cover" value="0"/>
+            <param name="block_size" value="2"/>
+            <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
+        </test>
+        <test>
+            <conditional name="method_cond">
+                <param name="method_select" value="blastx" />
+                <conditional name="frameshift_cond">
+                    <param name="frameshift_select" value="yes"/>
+                </conditional>
+            </conditional>
+            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
+            <conditional name="ref_db_source">
+                <param name="db_source" value="history"/>
+                <param name="reference_database" value="db.dmnd"/>
+            </conditional>
+            <conditional name="output">
+                <param name="outfmt" value="0"/>
+            </conditional>
+            <param name="sensitivity" value="0"/>
+            <param name="matrix" value="BLOSUM62"/>
+            <param name="comp-based-stat" value="1"/>
+            <param name="masking" value="1"/>
+            <conditional name="hit_filter">
+                <param name="hit_filter_select" value="top"/>
+                <param name="top" value="10" />
+            </conditional>
+            <conditional name="filter_score">
+                <param name="filter_score_select" value="score"/>
+                <param name="evalue" value="1" />
+            </conditional>
+            <param name="id" value="0"/>
+            <param name="query_cover" value="0"/>
+            <param name="block_size" value="2"/>
+            <output name="blast_tabular" file="diamond_results.pairwise"/>
+        </test>
+        <test>
+            <conditional name="method_cond">
+                <param name="method_select" value="blastp" />
+            </conditional>
+            <param name="query" value="protein.fasta" ftype="fasta"/>
+            <conditional name="ref_db_source">
+                <param name="db_source" value="history"/>
+                <param name="reference_database" value="db-wtax.dmnd"/>
+            </conditional>
+            <conditional name="output">
+                <param name="outfmt" value="100"/>
+            </conditional>
+            <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
+        </test>
     </tests>
-
     <help>
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