diff macros.xml @ 9:f921014aba5a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"

--- a/macros.xml	Mon Mar 22 13:21:23 2021 +0000
+++ b/macros.xml	Sat Nov 27 09:48:10 2021 +0000
@@ -1,9 +1,9 @@
 <macros>
-    <token name="@VERSION@">2.0.8</token>
+    <token name="@TOOL_VERSION@">2.0.8</token>
 
     <xml name="requirements">
         <requirements>
-          <requirement type="package" version="@VERSION@">diamond</requirement>
+          <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
         </requirements>
     </xml>
 
@@ -69,6 +69,7 @@
                     <option value="cigar">Cigar</option>
                     <yield/>
                 </param>
+                <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/>
             </when>
             <when value="100">
                 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
@@ -99,11 +100,11 @@
     </xml>
 
     <xml name="block_size_low_sens">
-        <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="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
     </xml>
 
     <xml name="block_size_hi_sens">
-        <param name="block_size" argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
+        <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
     </xml>
 
     <xml name="citations">
@@ -145,11 +146,16 @@
         #else if $output.outfmt == "6"
             --outfmt '6' #echo ' '.join(str($output.fields).split(','))
             --out '$blast_tabular'
+            --unal $output.unal
         #else if $output.outfmt == "100"
             --outfmt '100'
+            $output.salltitles
+            $output.sallseqid
             --out output.daa
         #else if $output.outfmt == "101"
             --outfmt '101'
+            $output.salltitles
+            $output.sallseqid
             --out '$sam_output'
         #else if $output.outfmt == "102"
             --outfmt '102'