hifiasm: version bump 0.19.7, add scaff options to wrapper (#1336)

* wrapper update for 0.19.7 * clean up * fixed conditional to make more sense
bgruening · Oct 13, 2023 · dfa4414 · dfa4414
1 parent 80417bf
commit dfa4414
Showing 1 changed file with 17 additions and 1 deletion.
diff --git a/tools/hifiasm/hifiasm.xml b/tools/hifiasm/hifiasm.xml
@@ -1,7 +1,7 @@
 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.19.5</token>
+        <token name="@TOOL_VERSION@">0.19.7</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
         <xml name="reads">
@@ -115,6 +115,12 @@
                 --n-hap $purge_options.n_hap
             #end if
         #end if
+        #if str($scaffolding_options.scaffold_selector) == 'set':
+            --dual-scaf 
+            #if $scaffolding_options.scaf_gap:
+                --scaf-gap $scaffolding_options.scaf_gap
+            #end if
+        #end if
 
         #if str($hic_partition.hic_partition_selector) == 'set':
             --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) }
@@ -273,6 +279,16 @@
                 </param>
             </when>
         </conditional>
+        <conditional name="scaffolding_options">
+            <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding">
+                <option value="blank">No scaffolding (default)</option>
+                <option value="set">Turn on hifiasm scaffolding</option>
+            </param>
+            <when value="blank" />
+            <when value="set">
+                <param argument="--scaf-gap" type="integer" min="1" value="3000000" optional="true" label="Max scaffolding gap size" help="Set the max gap size of scaffolds (default is 3,000,000)" />
+            </when>
+        </conditional>
         <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no" /> 
         <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no" /> 
     </inputs>