diff spaln.xml @ 2:dd0cd2319ae5 draft

"planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"

--- a/spaln.xml	Thu Jul 16 07:57:10 2020 -0400
+++ b/spaln.xml	Fri Nov 19 10:09:15 2021 +0000
@@ -38,6 +38,8 @@
             #if str($adv.max_gene_length).strip() != ''
                 -XG'${adv.max_gene_length}'
             #end if
+            $adv.format_remote_queries
+            $adv.salvage_mode
         #end if
         '$genome' '$query' >'$output1' 
     ]]></command>
@@ -90,6 +92,8 @@
             <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" />
             <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" />
             <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" />
+            <param argument="-yX" name="format_remote_queries" type="boolean" checked="false" truevalue="-yX" falsevalue="" label="Format for remote queries" help="More sensitive but less economic than the default" />
+            <param argument="-XS" name="salvage_mode" type="boolean" checked="false" truevalue="-XS" falsevalue="" label="Activate salvage mode" help="Examine all positively scored blocks. Considerably slow." />
         </when>
     </conditional>
     </inputs>