# HG changeset patch
# User iuc
# Date 1754057078 0
# Node ID cb132bfc5ab18da42e67039ecf449cf3ebb0d1d1
# Parent  eca7ac1eb423206c7cebc33c91f3352d30db8659
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d365d03a21ea7467b9e29bf7f2751e96fcd9ada1

diff -r eca7ac1eb423 -r cb132bfc5ab1 lastal.xml
--- a/lastal.xml	Mon Oct 23 20:45:02 2023 +0000
+++ b/lastal.xml	Fri Aug 01 14:04:38 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy2" profile="20.01">
+<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>finds local alignments between query sequences, and reference sequences.</description>
     <macros>
         <import>macros_last.xml</import>
@@ -371,9 +371,6 @@
                 <param name="database" value="humdb-sanger"/>
             </conditional>
             <param name="query_seq" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
-            <section name="lastal">
-                <param name="Q" value="1"/>
-            </section>
             <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/>
         </test>        
     </tests>
diff -r eca7ac1eb423 -r cb132bfc5ab1 lastdb.xml
--- a/lastdb.xml	Mon Oct 23 20:45:02 2023 +0000
+++ b/lastdb.xml	Fri Aug 01 14:04:38 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>prepares sequences for subsequent comparison and alignment using lastal.</description>
     <macros>
         <import>macros_last.xml</import>
@@ -164,11 +164,11 @@
                 <conditional name="sequences_type">
                     <param name="protein" value="-p"/> 
                 </conditional>
-            </section>
-            <section name="lastdb_advanced">
-                <conditional name="seeds">
-                    <param name="u" value="MURPHY10"/>
-                </conditional>
+                <section name="lastdb_advanced">
+                    <conditional name="seeds">
+                        <param name="u" value="MURPHY10"/>
+                    </conditional>
+                </section>
             </section>
             <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
                 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
@@ -183,7 +183,6 @@
         <test>
             <param name="input_files" value="humanMito.fq.gz" ftype="fastqsanger.gz"/>
             <section name="lastdb">
-                <param name="Q" value="1"/>
                 <section name="repeats">
                     <param name="uppercase" value="0"/>
                     <param name="simple_repeat" value="1"/>
diff -r eca7ac1eb423 -r cb132bfc5ab1 lastsplit.xml
--- a/lastsplit.xml	Mon Oct 23 20:45:02 2023 +0000
+++ b/lastsplit.xml	Fri Aug 01 14:04:38 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description>
     <macros>
         <import>macros_last.xml</import>
diff -r eca7ac1eb423 -r cb132bfc5ab1 lasttrain.xml
--- a/lasttrain.xml	Mon Oct 23 20:45:02 2023 +0000
+++ b/lasttrain.xml	Fri Aug 01 14:04:38 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
     <macros>
         <import>macros_last.xml</import>
diff -r eca7ac1eb423 -r cb132bfc5ab1 macros_last.xml
--- a/macros_last.xml	Mon Oct 23 20:45:02 2023 +0000
+++ b/macros_last.xml	Fri Aug 01 14:04:38 2025 +0000
@@ -1,5 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1205</token>
+    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@PROFILE@">24.0</token>
     <token name="@LAST_HELP@"><![CDATA[
         Documentation : https://gitlab.com/mcfrith/last
 
diff -r eca7ac1eb423 -r cb132bfc5ab1 maf-convert.xml
--- a/maf-convert.xml	Mon Oct 23 20:45:02 2023 +0000
+++ b/maf-convert.xml	Fri Aug 01 14:04:38 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>read MAF-format alignments and write them in another format.</description>
     <macros>
         <import>macros_last.xml</import>
@@ -18,9 +18,9 @@
         #end if
 
         #if $maf_convert.output_type.output_format == 'sam'
-            $maf_convert.output_type.sam_file.dictionary
-            #if $maf_convert.output_type.sam_file.dictionary == '-d'
-                -f $maf_convert.output_type.sam_file.f
+            #if $maf_convert.output_type.f
+                -d
+                -f $maf_convert.output_type.f
             #end if
             #if $maf_convert.output_type.readfile != ''
                 -r $maf_convert.output_type.r
@@ -68,16 +68,7 @@
                     <param argument="-j" type="integer" value="1" label="Join neighboring alignments" help="Join neighboring alignments if they are co-linear and separated by at most N letters."/>
                 </when>
                 <when value="sam">
-                    <conditional name="sam_file">
-                        <param name="dictionary" argument="-d" type="select" label="Include dictionary of sequence lengths in sam format">
-                            <option value="-d">Yes</option>
-                            <option value="" selected="true">No</option>
-                        </param>
-                        <when value=""/>
-                        <when value="-d">
-                            <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" />
-                        </when>
-                    </conditional>			    
+                    <param argument="-f" type="data" format="sam" optional="true" label="Sequence dictionary" help="Include dictionary of sequence lengths in sam format. Also toggles -d"/>
                     <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/>
                 </when>
                 <when value="tab"/>