# HG changeset patch
# User bgruening
# Date 1724354424 0
# Node ID 8e649f27aa0dda757c545f52f0d47506f12c6627
# Parent  bf28a8cff401735fd2b8d046587c60622d8f089a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443

diff -r bf28a8cff401 -r 8e649f27aa0d macros.xml
--- a/macros.xml	Wed Mar 20 07:34:52 2024 +0000
+++ b/macros.xml	Thu Aug 22 19:20:24 2024 +0000
@@ -1,6 +1,5 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">7.520</token>
+    <token name="@TOOL_VERSION@">7.526</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <!-- currently, the fasta3 executable is named according to its major version
@@ -18,15 +17,15 @@
         </requirements>
     </xml>
     <xml name="weighti_param">
-        <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
+        <param argument="--weighti" type="float" min="1" max="100" value="2.7" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
     </xml>
     <xml name="parttree_parameters">
-        <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/>
-        <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/>
-        <param argument="--groupsize" type="integer" value="-1" min="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/>
+        <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is built this number of times in the progressive stage."/>
+        <param argument="--partsize" type="integer" min="0" max="1000" value="50" label="Number of partitions in the PartTree algorithm."/>
+        <param argument="--groupsize" type="integer" min="-1" value="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/>
     </xml>
     <xml name="misc_scoring_scheme">
-        <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" />
+        <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?"/>
         <conditional name="gap_costs">
             <param name="use_defaults" type="select" label="Configure gap costs">
                 <option value="yes">Use default values</option>
@@ -42,7 +41,7 @@
     <xml name="global_align_options">
         <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true">
             <param argument="--unalignlevel" type="float" min="0" max="0.8" value="0" label="Over-alignment correction factor" help="The higher this factor the more likely will unrelated sequence stretches in globally related sequences be left unaligned. The default of 0 turns over-alignment correction off, turning it on increases run time."/>
-            <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/>
+            <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for &gt; ~1000 sequences."/>
         </section>
     </xml>
     <xml name="citations">
diff -r bf28a8cff401 -r 8e649f27aa0d mafft-add.xml
--- a/mafft-add.xml	Wed Mar 20 07:34:52 2024 +0000
+++ b/mafft-add.xml	Thu Aug 22 19:20:24 2024 +0000
@@ -1,20 +1,12 @@
-<?xml version="1.0" encoding="UTF-8"?>
 <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-  <description>Align a sequence,alignment or fragments to an existing alignment.</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="biotools"/>
-  <expand macro="requirements"/>
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-    <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-  </stdio>
-  <version_command>    <![CDATA[
-    mafft --version
-    ]]>
-  </version_command>
-  <command>
+    <description>Align a sequence,alignment or fragments to an existing alignment.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <version_command>mafft --version</version_command>
+    <command detect_errors="exit_code">
     <![CDATA[
       sh mk_symlinks.sh &&
       mafft
@@ -35,53 +27,53 @@
       #end if
     ]]>
   </command>
-  <configfiles>
-    <configfile filename="mk_symlinks.sh"><![CDATA[
+    <configfiles>
+        <configfile filename="mk_symlinks.sh"><![CDATA[
 mkdir input_dir &&  
 ln -s '$inputSequences' input_dir/sequence &&
 ln -s '$inputAlignment' input_dir/alignment
     ]]></configfile>
-  </configfiles>
-  <inputs>
-    <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
-    <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
-    <conditional name="sequences">
-      <param name="sequenceType" type="select" label="What do you want to add to the alignment?" >
-        <option value="singleseq">A single sequence</option>
-        <option value="frags" selected="true">Fragments</option>
-        <option value="group">An alignment</option>
-      </param>
-      <when value='singleseq'>
-        <param name="preservegap" type="select" label="Preserve the original alignment." help="Keep the given alignment unchanged .If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved.">
-          <option value="--add" selected="true" >Yes (--add)</option>
-          <option value="--seed">No (--seed)</option>
-        </param>
-      </when>
-      <when value='frags'/>
-      <when value='group'/>
-    </conditional>
-    <param argument="--keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged.  Insertions at the additional sequences are deleted" />
-    <param argument="--mapout" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of position." help="Output a correspondence table of positions, sequence.map, between before and after the calculation.  The mapout option automatically turns on the keeplength option, to keep the numbering of sites in the reference alignment" />
-    <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences."  />
-  </inputs>
-  <outputs>
-    <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
-    <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
-      <filter>map == True</filter>
-    </data>
-  </outputs>
-  <tests>
-    <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=""/>
-      <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
-    </test>
-  </tests>
-  <help>
+    </configfiles>
+    <inputs>
+        <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
+        <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
+        <conditional name="sequences">
+            <param name="sequenceType" type="select" label="What do you want to add to the alignment?">
+                <option value="singleseq">A single sequence</option>
+                <option value="frags" selected="true">Fragments</option>
+                <option value="group">An alignment</option>
+            </param>
+            <when value="singleseq">
+                <param name="preservegap" type="select" label="Preserve the original alignment." help="Keep the given alignment unchanged .If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved.">
+                    <option value="--add" selected="true">Yes (--add)</option>
+                    <option value="--seed">No (--seed)</option>
+                </param>
+            </when>
+            <when value="frags"/>
+            <when value="group"/>
+        </conditional>
+        <param argument="--keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged.  Insertions at the additional sequences are deleted"/>
+        <param argument="--mapout" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of position." help="Output a correspondence table of positions, sequence.map, between before and after the calculation.  The mapout option automatically turns on the keeplength option, to keep the numbering of sites in the reference alignment"/>
+        <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences."/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
+        <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
+            <filter>map == True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <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=""/>
+            <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
+        </test>
+    </tests>
+    <help>
     <![CDATA[
 Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement.
 
@@ -95,5 +87,5 @@
 
     ]]>
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff -r bf28a8cff401 -r 8e649f27aa0d mafft.xml
--- a/mafft.xml	Wed Mar 20 07:34:52 2024 +0000
+++ b/mafft.xml	Thu Aug 22 19:20:24 2024 +0000
@@ -6,12 +6,8 @@
     </macros>
     <expand macro="biotools"/>
     <expand macro="requirements" />
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-    </stdio>
-    <version_command><![CDATA[mafft --version]]></version_command>
-    <command><![CDATA[
+    <version_command>mafft --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
   ## Concatenate all input datasets no matter how they were provided
   bash inputs.sh &&
 
@@ -170,7 +166,7 @@
             </when>
             <when value="merge">
                 <repeat name="batches" title="Input batch" default="1" min="1">
-                    <param name="inputs" multiple="true" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
+                    <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format." multiple="true"/>
                 </repeat>
             </when>
         </conditional>
@@ -187,7 +183,7 @@
                         <option value="--kimura">Kimura</option>
                     </param>
                     <when value="--kimura">
-                        <param argument="--kimura" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
+                        <param name="coefficient" argument="--kimura" type="integer" min="1" value="200" label="PAM value of the matrix" />
                     </when>
                 </conditional>
                 <expand macro="misc_scoring_scheme" />
@@ -201,7 +197,7 @@
                         <option value="custom">custom matrix</option>
                     </param>
                     <when value="--bl">
-                        <param argument="--bl" name="coefficient" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
+                        <param name="coefficient" argument="--bl" type="select" label="Coefficient of the BLOSUM matrix" display="radio">
                             <option value="30">30</option>
                             <option value="45">45</option>
                             <option value="62" selected="true">62</option>
@@ -209,10 +205,10 @@
                         </param>
                     </when>
                     <when value="--jtt">
-                        <param argument="--jtt" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
+                        <param name="coefficient" argument="--jtt" type="integer" min="1" value="200" label="PAM value of the matrix" />
                     </when>
                     <when value="--tm">
-                        <param argument="--tm" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix"/>
+                        <param name="coefficient" argument="--tm" type="integer" min="1" value="200" label="PAM value of the matrix"/>
                     </when>
                     <when value="custom">
                         <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/>
@@ -267,7 +263,7 @@
                                 <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option>
                             </param>
                             <when value="--6merpair">
-                                <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is build this number of times in the progressive stage."/>
+                                <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is build this number of times in the progressive stage."/>
                             </when>
                             <when value="--globalpair">
                                 <expand macro="global_align_options"/>
@@ -312,7 +308,7 @@
                     </when>
                 </conditional>
                 <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true">
-                    <param argument="--maxiterate" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
+                    <param argument="--maxiterate" type="integer" min="0" max="1000" value="0" label="Maximum number of iterations" help="1000 for maximum quality" />
                     <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
                     <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
                 </section>
@@ -391,7 +387,7 @@
                 <param name="type" value="mafft-fftns"/>
             </conditional>
             <param name="outputFormat" value="--clustalout"/>
-            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" />
+            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" lines_diff="2" />
         </test>
         <test expect_num_outputs="1" >
             <conditional name="input">
@@ -437,7 +433,7 @@
                 </section>
             </conditional>
             <param name="outputFormat" value="--clustalout"/>
-            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln">
+            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln" lines_diff="2">
             </output>
         </test>
         <test expect_num_outputs="1">