diff nextalign.xml @ 8:1c785a6b4d90 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 017e25729a8ffd3722e87dfdf10ff4fd99c0babd"

--- a/nextalign.xml	Tue Nov 30 09:21:44 2021 +0000
+++ b/nextalign.xml	Mon Dec 13 17:02:52 2021 +0000
@@ -34,10 +34,6 @@
     --nuc-min-seeds '${nuc_min_seeds}'
     --nuc-seed-spacing '${nuc_seed_spacing}'
     --nuc-mismatches-allowed '${nuc_mismatches_allowed}'
-    --aa-seed-length '${aa_seed_length}'
-    --aa-min-seeds '${aa_min_seeds}'
-    --aa-seed-spacing '${aa_seed_spacing}'
-    --aa-mismatches-allowed '${aa_mismatches_allowed}'
     ]]></command>
     <inputs>
         <expand macro="reference"/>
@@ -97,16 +93,6 @@
         <param argument="--nuc-mismatches-allowed" type="integer" value="3" min="0"
             label="Maximum number of mismatching nucleotides."
             help="Maximum number of mismatching nucleotides allowed for a seed to be considered a match." />
-        <param argument="--aa-seed-length" type="integer" value="12" min="1"
-            label="Seed length for aminoacid alignment" />
-        <param argument="--aa-min-seeds" type="integer" value="10" min="1"
-            label="Minimum number of seeds to search for during aminoacid alignment."
-            help="Relevant for short sequences. In long sequences, the number of seeds is determined by the aminoacid seed spacing." />
-        <param argument="--aa-seed-spacing" type="integer" value="100" min="0"
-            label="Spacing between seeds during aminoacid alignment." />
-        <param argument="--aa-mismatches-allowed" type="integer" value="2" min="0"
-            label="Maximum number of mismatching aminoacids."
-            help="Maximum number of mismatching aminoacids allowed for a seed to be considered a match." />
     </inputs>
     <outputs>
         <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>