# HG changeset patch
# User bgruening
# Date 1741193196 0
# Node ID 1233363389c117cb2597260643ae0ff340711759
# Parent  8e649f27aa0dda757c545f52f0d47506f12c6627
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 16082a6848975215c251a4440c7c3c359fc7d34c

diff -r 8e649f27aa0d -r 1233363389c1 macros.xml
--- a/macros.xml	Thu Aug 22 19:20:24 2024 +0000
+++ b/macros.xml	Wed Mar 05 16:46:36 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">7.526</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
     <!-- currently, the fasta3 executable is named according to its major version
     => needs updating together with the package requirement! -->
diff -r 8e649f27aa0d -r 1233363389c1 mafft-add.xml
--- a/mafft-add.xml	Thu Aug 22 19:20:24 2024 +0000
+++ b/mafft-add.xml	Wed Mar 05 16:46:36 2025 +0000
@@ -17,11 +17,11 @@
       #elif $sequences.sequenceType == 'group'
         --addprofile input_dir/sequence
       #end if
-      $keeplength 
-      $mapout 
+      $keeplength
+      $mapout
       $reorder
       input_dir/alignment > '$outputAlignment'
-      
+
       #if $mapout
         && mv input_dir/sequence.map '$outputmap'
       #end if
@@ -29,7 +29,7 @@
   </command>
     <configfiles>
         <configfile filename="mk_symlinks.sh"><![CDATA[
-mkdir input_dir &&  
+mkdir input_dir &&
 ln -s '$inputSequences' input_dir/sequence &&
 ln -s '$inputAlignment' input_dir/alignment
     ]]></configfile>
@@ -66,10 +66,12 @@
         <test expect_num_outputs="1">
             <param name="inputSequences" value="add_seq.fa"/>
             <param name="inputAlignment" value="mafft_default.aln"/>
-            <param name="sequenceType" value="singleseq"/>
-            <param name="preservegap" value="--add"/>
-            <param name="keeplength" value="--keeplength"/>
-            <param name="mapout" value=""/>
+            <conditional name="sequences">
+                <param name="sequenceType" value="singleseq"/>
+                <param name="preservegap" value="--add"/>
+            </conditional>
+            <param name="keeplength" value="True"/>
+            <param name="mapout" value="False"/>
             <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
         </test>
     </tests>
diff -r 8e649f27aa0d -r 1233363389c1 mafft.xml
--- a/mafft.xml	Thu Aug 22 19:20:24 2024 +0000
+++ b/mafft.xml	Wed Mar 05 16:46:36 2025 +0000
@@ -107,6 +107,7 @@
 
   ## handle scoring matrix
   $datatype_selection.datatype
+  $anysymbol
   #if $datatype_selection.datatype != ""
     #if $datatype_selection.scoring_matrix.type == "custom"
       --aamatrix '$datatype_selection.scoring_matrix.aamatrix'
@@ -143,7 +144,7 @@
   #if $input.mapping == "implicit"
     #for $batch in $input.batches:
 cat $batch.inputs >> input.fa
-      #end for 
+      #end for
   #elif $input.mapping == "merge"
     #for $batch in $input.batches:
       #for $dataset in $batch.inputs:
@@ -217,6 +218,7 @@
                 <expand macro="misc_scoring_scheme" />
             </when>
         </conditional>
+        <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.">
                 <option value="mafft --auto">Auto</option>
@@ -343,6 +345,17 @@
             </conditional>
             <output name="outputAlignment" ftype="fasta" file="mafft_default.aln"/>
         </test>
+        <!-- test with anysymbol parameter -->
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="amino_withU.fa"/>
+                </repeat>
+            </conditional>
+            <param name="anysymbol" value="True"/>
+            <output name="outputAlignment" ftype="fasta" file="mafft_amino_withU.aln"/>
+        </test>
         <!-- test autodetection of suitable algorithm from input; expected to choose L-INS-i -->
         <test expect_num_outputs="1">
             <conditional name="input">
diff -r 8e649f27aa0d -r 1233363389c1 test-data/amino_withU.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amino_withU.fa	Wed Mar 05 16:46:36 2025 +0000
@@ -0,0 +1,56 @@
+>CALJE_DJ01Gene08198
+MDRVKNQNEDLLSGVVPLMKLLCLTVIGLVLAHPKIQIVPRATFKLLSKLVFALFLPCLI
+FVHLGESVTLNSVLLWWFVPVNVLISTAIGCALGYIVAIICRPPPQFYRFAVIMTGFGNT
+GNLPIAIVGSVCHSSENPFGPDCHRTGVAYVSFAQWVAVILVYTLVYHMMEPPMQYYEIV
+SEENEIQEETVNNISRPLLHEAEWPGMVDKETVHSKTPFIARVFMSISGSSQNTFPDLDL
+TEDGGAGPSSPKSLRCLAEPKVVRRIRIVAEETPIRHILQPPTIASLLALIVGMVPLFRD
+FVFGTDAPLSFFTDSLEILAGAVVPSVMLILGGMLAEGPNDSALGTRTMIGITVARLLVL
+PLVGIGVVALADKLNFLVEGDQMYRFVLLLQYTTPSAILLGAIASLRVMLSRKLRHSCSG
+STSVQUSSNSICNLLILLHSLADEDVGASQSGELIKGTDATRHQLFPGKDAGFAREQRHG
+FHAAEVFIAPCSQKEEKMLFEARRLVRWGFHEPHGPRHAAFQPWPDLSRARKHCLAPEAG
+VDSIAKSAHRSHFSAFSPTP
+>CALJE_DJ01Gene07324
+MHQKRDIDPADLWLPYSFRSSNMISLATVYHVLEATVPLYAAMMLAYLSIKWWKLFTPDQ
+CTGINKFVAKFSVPLLSFHVISTNNPYQMNLKLLFSDSMQKILALLFFAVISKACFRGSL
+DWLITGFSLSTLPNTLIVGIPLLKDLYGDEAAKLLGQIIVLQSLVWYTLLLFLFEFRVAK
+AVAANRNDNTGELEASGGMQPKPEEDEAKTLSMRSIKSLLMKSLLILCMVGKKLMINPNT
+YASLAGFVWALISFRWGIELPLMIRSCISILSDGGLGMAMFSLGLFTASQSSIIACGTRM
+MVLSMGLRFIVGPALIAIPSYAIGMRATLLKVAIVQAALPQGIVPWVFAKEYGVQPDILS
+TGVIIGMIIAVPIALAYYSILDHN
+>CALJE_DJ01Gene04286
+MITWHDLYTVLTAVVPLYVAMILAYGSVRWWRIFSPDQCSGINRFVAIFAVPLLSFHFIS
+TNNPYTMNFRFIAADTLQKLIVLSALAAWARLSSRGSLDWAITVFSLATLPNTLVMGIPL
+LIAMYGSFSGSLMVQIVVLQCIIWYTLLLFLFEYRAARLLIADQFPDTAASIVSFRVDSD
+VVSLDGGRDLLQADAEVGGDGKIHVTVRRSNASRRSVSMAMTPRPSNLTGAEIYSLSSSR
+NPTPRGSNFNHSDFFAMVGGAPPPLRPSNFGPADLYSLHSSRGPTPRPSNFDDGAAVGSP
+RFVHYPAPNPEISASAPVTKKPTPTNPAPPSTAAATQQQNRAAHHDAKELHMFVWSSSAS
+PVSEVGGLHVFGGADFAAPDLAGRPDHGGAKEIRMLIPTDLPQNGGTKGVAIPEGEDYGG
+GGEDFSFGGGKGLEDLVGRDKENGPEGLSKLGSSSTAELHPKGGGGPSDGAKQAHPQMPP
+ASVMTRLILIMVWRKLIRNPNTYSSLIGLIWSLVAFRWHVTMPKIVEKSISILSDAGLGM
+AMFSLGLFMALQPKIIACGNSVATFAMAVRFLTGPAVMAAASIAVGLRGVLLHVAIVQAA
+LPQGIVPFVFAKEYNVHPAILSTAVIFGMLIALPITLVYYIILGL
+>CALJE_DJ01Gene08527
+MISLVIVYHVLEATVPLYAAMILAYLSVKWWKLFTPDQCTGINNFVAKFSVPLLSFHVIS
+PNNPYPINLKLLFSDSVQKILALLVFAVLSRPCFRGSLDWLITGFSTSTLPNTLIIGIPL
+LKGLYGDEAVKLLGQIIVLQSLVWNTLLLFLFEVRAAKAVAANPTDNTGELESSGGIQPK
+PEEDEVKCLLAGFIWALILFRWEVELPLIISKCISILSDGGLGMAMFSLGLFMASQSSII
+ASGTWMMVLSMGLRFIIGPALIAIPSYAIGLRATLLKVAIVQAALPQGIVPFVFAKEYSV
+HPDILSTGFKLDQGFLLADERAIEKIDAVELRENPDNEMGRSPESRRKGAVIVPIISDAI
+GADAGGGLFQAVSSAFRRPHC
+>CALJE_DJ01Gene19453
+MITGKDIYDVLAAIVPLYVAMILAYGSVRWWKIFTPDQCSGINRFVAVFAVPLLSFHFIS
+TNNPYAMNYHFIGADSLQKVVILFALFLWHNLSKRGNLDWTITLFSLSTLPNTLVMGIPL
+LRAMYGDFSGSLMVQIVVLQSVIWYTLMLFLFEYRGAKALISEQFPPDIAGSITSFRVDS
+DVVSLNGREPLQADAEIRQDGKLHVVVRRSTSSAARSMSSSYNKSHGLNSITSMTPRASN
+LTGVEIYSLQSSREPTPRASSFNQTDFYAMFSSKVTSPRPDPSKPALHQDIPAPKGLHAP
+SGNASPIRKAGTNGDLEIEDGCKSQEGKFPASPFVAQKKGTDTGGVAGLVENNHRMPPAS
+VMTRLILIMVWRKLIRNPNTYSSLLGLVWSLVSFRWNIEMPTIIKGSISILSDAGLGMAM
+FSLGLFMALQPKIIACGKSVAAFSMAVRFLTGPAVIAATSIAIGVRGVLLHVAIVQAALP
+QGIVPFVFAKEYNCHPDILSTAVIFGMLIALPITILYYVLLGV
+>CALJE_DJ01Gene20884
+MIGWEDVCKVVASMVPLYVALGLGYGSVRWWHVFTPDQCDAVNRLVFSFTLPFYAFEFAI
+HADPFSMNCRLIAADIIGKLIVILVLSLWAKCREGSHRCSWFITAFSLSTLNNSLVLGLP
+LLTSLYGPSVRGLVVQTTVMQAIIWLTLLLFMLEIKKAKGILLEESPMKEERSWPSFWCL
+MRMVWLKLALNPNFYASILGITWAFIANRWQLEMPSIMEGSVLVISRAGTGMAMFCIGLF
+MALQKKMLACGARLTALALVLRFVVGPATMAISAFAVGLHGDVLRLAIIQAALPQSVTSF
+IFAREYGLHADVLSTAVILGLLVCLPVLVAYNVLLGFVT
diff -r 8e649f27aa0d -r 1233363389c1 test-data/mafft_amino_withU.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_amino_withU.aln	Wed Mar 05 16:46:36 2025 +0000
@@ -0,0 +1,96 @@
+>CALJE_DJ01Gene08198
+MDRVKNQNE---------------------DLLSGVVPLMKLLCLTVIGLVLAHPKIQ--
+-IVPRATFKLLSKLVFALFLPCLIF--VHLGESVTLNSVLLWWFVPVNVLISTAIG----
+-CALGYIVAIICRPPPQFYRFAVIMTGFG-----NTGNLPIAIVGSVCHSSENPFGPDCH
+RTGVAYVSFAQWVAVILVYTLVYHMME------------PPMQYYEIVSEENEIQEETVN
+NISRPLLHEAEWPG------MVDKETVH--------------------------------
+-----------------SKTPFIARV-------FMSISG--------SSQNTFPDL----
+-------------------------------------------------DLTED------
+----GGAGPSSP-----------------------------KSLRCLAE-----------
+------------------------------------------------------------
+---------PKVVRRIRIVAEETPIRHILQPPTIASLLALIVGMVPLFRDFVFGTDAPLS
+FFTDSLEILAGAVVPSVMLILGGMLAEGPNDSALGTRTMIGITVARLLVLP---------
+------LVGIGVVALADKLNFLVEGDQMYRFVLLLQYTTPSAILLGAIASLRVMLSRKLR
+HSCSGSTSVQUSSNSICNLLILLHSLADEDVGASQSGELIK------GTDATRHQLFPGK
+DAGFAREQRHGFHAAEVFIAPC-SQKEEKMLFEARRLVRWGFHEPHGPRHAAFQPWPDLS
+RARKHCLAPEAGVD---SIAKSAHRSHFSAFSPTP
+>CALJE_DJ01Gene07324
+MHQKRDIDPADLWLPYSFRSSNMISLATVYHVLEATVPLY-------AAMMLAYLSIKWW
+KLFTPDQCTGINKFVAKFSVPLLSFHVISTNNPYQMNLKLLFSDSMQKILALLFFAVISK
+ACFRGS--------------LDWLITGFSLSTLPNTLIVGIPLLKDL-------YGDEAA
+KLLGQIIV----LQSLVWYTLLLFLFEFRVAKAVAA------------------------
+------------------------------------------------------------
+-----------------NRND---------------NTG-----ELEASGGMQPKP----
+---------------------------------------------------EED--EAKT
+LSM--------------------------------------RSIKSLLMKSL--------
+------------------------------------------------------------
+-----------------LILCMVGKKLMINPNTYASLAGFVWALIS----FRWGIELP-L
+MIRSCISILSDGGLGMAMFSLGLFTASQSSIIACGTRMMVLSMGLRFIVGPALIAIPSYA
+IGMRATLLKVAIVQAA-----LPQG--IVPWVFAKEYGVQPDIL----------------
+-----STGVII-------------------------GMIIA-------------------
+-------------------VPI--------------------------------------
+-----------------ALAYYSILDHN-------
+>CALJE_DJ01Gene04286
+----------------------MITWHDLYTVLTAVVPLY-------VAMILAYGSVRWW
+RIFSPDQCSGINRFVAIFAVPLLSFHFISTNNPYTMNFRFIAADTLQKLIVLSALAAWAR
+LSSRGS--------------LDWAITVFSLATLPNTLVMGIPLLIAM-------YGSFSG
+SLMVQIVV----LQCIIWYTLLLFLFEYRAARLLIADQF-PDTAASIVSFRVDSDVVSLD
+GGRDLLQADAEVGGDGKIHVTVRRSNAS-RRSVS------------MAMTPRPSNLTGAE
+IYSLSSSRNPTPRGSNFNHSDFFAMVGGAPPPLRPSNFGPADLYSLHSSRGPTPRPSNFD
+DGAAVGSPRFVHYPAPNPEISASAPVTKKPTPTNPAPPSTAAATQQQNRAAHHD---AKE
+LHMFVWSSSASPVSEVGGLHVFGGADFAAPDLAGRPDHGGAKEIRMLIPTDLPQNGGTKG
+VAIPEGEDYGGGGEDFSFGGGKGLEDLVGRDKENGPEGLSKLGSSSTAELHPKGGGGPSD
+GAKQAHPQMPPASVMTRLILIMVWRKLIRNPNTYSSLIGLIWSLVA----FRWHVTMP-K
+IVEKSISILSDAGLGMAMFSLGLFMALQPKIIACGNSVATFAMAVRFLTGPAVMAAASIA
+VGLRGVLLHVAIVQAA-----LPQG--IVPFVFAKEYNVHPAIL----------------
+-----STAVIF-------------------------GMLIA-------------------
+-------------------LPI--------------------------------------
+-----------------TLVYYIILGL--------
+>CALJE_DJ01Gene08527
+----------------------MISLVIVYHVLEATVPLY-------AAMILAYLSVKWW
+KLFTPDQCTGINNFVAKFSVPLLSFHVISPNNPYPINLKLLFSDSVQKILALLVFAVLSR
+PCFRGS--------------LDWLITGFSTSTLPNTLIIGIPLLKGL-------YGDEAV
+KLLGQIIV----LQSLVWNTLLLFLFEVRAAKAVAA------------------------
+------------------------------------------------------------
+-----------------NPTD---------------NTG-----ELESSGGIQPKP----
+---------------------------------------------------EED--EVKC
+L-----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------LAGFIWALIL----FRWEVELP-L
+IISKCISILSDGGLGMAMFSLGLFMASQSSIIASGTWMMVLSMGLRFIIGPALIAIPSYA
+IGLRATLLKVAIVQAA-----LPQG--IVPFVFAKEYSVHPDIL----------------
+-----STGFKLD-----------------------QGFLLADERAIEKIDAVELRENPDN
+EMGRSPESRR----KGAVIVPIISD-----------------------------------
+-----AIGADAGGGLFQAVSSAFRRPHC-------
+>CALJE_DJ01Gene19453
+----------------------MITGKDIYDVLAAIVPLY-------VAMILAYGSVRWW
+KIFTPDQCSGINRFVAVFAVPLLSFHFISTNNPYAMNYHFIGADSLQKVVILFALFLWHN
+LSKRGN--------------LDWTITLFSLSTLPNTLVMGIPLLRAM-------YGDFSG
+SLMVQIVV----LQSVIWYTLMLFLFEYRGAKALISEQFPPDIAGSITSFRVDSDVVSLN
+-GREPLQADAEIRQDGKLHVVVRRSTSSAARSMSSSYNKSHGLNSITSMTPRASNLTGVE
+IYSLQSSREPTPRASSFNQTDFYAMF---------------------SSKVTSPRP----
+---------------------------------DPSKP-----------ALHQDIPAPKG
+LH--APSGNASPIRKAG-----TNGDLEIED--------GCKSQEGKFP-------ASPF
+VAQKKGTDTGGVA-----------------------------------------------
+GLVENNHRMPPASVMTRLILIMVWRKLIRNPNTYSSLLGLVWSLVS----FRWNIEMP-T
+IIKGSISILSDAGLGMAMFSLGLFMALQPKIIACGKSVAAFSMAVRFLTGPAVIAATSIA
+IGVRGVLLHVAIVQAA-----LPQG--IVPFVFAKEYNCHPDIL----------------
+-----STAVIF-------------------------GMLIA-------------------
+-------------------LPI--------------------------------------
+-----------------TILYYVLLGV--------
+>CALJE_DJ01Gene20884
+----------------------MIGWEDVCKVVASMVPLY-------VALGLGYGSVRWW
+HVFTPDQCDAVNRLVFSFTLPFYAFEFAIHADPFSMNCRLIAADIIGKLIVILVLSLWAK
+-CREGSH------------RCSWFITAFSLSTLNNSLVLGLPLLTSL-------YGPSVR
+GLVVQTTV----MQAIIWLTLLLFMLEIKKAKGILLEE----------------------
+------------------------------------------------------------
+----------------------------------------------------SPMK----
+---------------------------------------------------EER------
+---------SWP------------------------------------------------
+----------------SFW-----------------------------------------
+-----------------CLMRMVWLKLALNPNFYASILGITWAFIA----NRWQLEMP-S
+IMEGSVLVISRAGTGMAMFCIGLFMALQKKMLACGARLTALALVLRFVVGPATMAISAFA
+VGLHGDVLRLAIIQAA-----LPQS--VTSFIFAREYGLHADVL----------------
+-----STAVIL-------------------------GLLVC-------------------
+-------------------LPV--------------------------------------
+-----------------LVAYNVLLGFVT------