diff mafft.xml @ 18:0a507f4bd19a draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3216eed8c66b2fff7c571ab27d3f1e6aaddc186f

--- a/mafft.xml	Wed Mar 05 16:46:36 2025 +0000
+++ b/mafft.xml	Mon Jul 14 18:16:36 2025 +0000
@@ -105,6 +105,12 @@
     #end if
   #end if
 
+  #if $seed
+    #for $s in $seed:
+      --seed '$s'
+    #end for
+  #end if
+
   ## handle scoring matrix
   $datatype_selection.datatype
   $anysymbol
@@ -218,6 +224,7 @@
                 <expand macro="misc_scoring_scheme" />
             </when>
         </conditional>
+        <param argument="--seed" type="data" format="fasta" optional="true" multiple="true" label="Use a seed alignment?" help="The --seed option can be used for adding unaligned sequences into a highly reliable alignment (seed) consisting of a small number of sequences.  In this option, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved.  If the given alignment (including the gap pattern) has to be completely preserved, use mafft-add."/>
         <param argument="--anysymbol" type="boolean" truevalue="--anysymbol" falsevalue="" checked="False" label="Support unusual characters?" help="e.g., U as selenocysteine in protein sequence; i as inosine in nucleotide sequence" />
         <conditional name="flavour">
             <param name="type" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section. With 'Auto', the tool automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size from few to many respectively. Default setting: FFT-NS-2.">
@@ -487,6 +494,20 @@
                 <metadata name="sequences" value="39"/>
             </output>
         </test>
+        <!-- test with seed alignments -->
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+            </conditional>
+            <conditional name="flavour">
+                <param name="type" value="mafft-linsi"/>
+            </conditional>
+            <param name="seed" value="seed.aln,seed2.aln"/>
+            <output name="outputAlignment" ftype="fasta" file="mafft_seed_out.aln"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**