diff mafft-add.xml @ 15:bf28a8cff401 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 2f6456c314c010fd73f5eeaf809a9afce47353af

--- a/mafft-add.xml	Tue Oct 31 15:48:53 2023 +0000
+++ b/mafft-add.xml	Wed Mar 20 07:34:52 2024 +0000
@@ -16,43 +16,53 @@
   </version_command>
   <command>
     <![CDATA[
+      sh mk_symlinks.sh &&
       mafft
       #if $sequences.sequenceType == 'singleseq'
-        $sequences.preservegap  '$inputSequences'
+        $sequences.preservegap input_dir/sequence
       #elif $sequences.sequenceType == 'frags'
-        --addfragments '$inputSequences'
+        --addfragments input_dir/sequence
       #elif $sequences.sequenceType == 'group'
-        --addprofile '$inputSequences'
+        --addprofile input_dir/sequence
       #end if
-      $keeplength $map $reorder
-      '$inputAlignment'
-      > '$outputAlignment'
-      #if $map == '--mapout'
-        && mv '${inputSequences}.map' '$outputmap'
+      $keeplength 
+      $mapout 
+      $reorder
+      input_dir/alignment > '$outputAlignment'
+      
+      #if $mapout
+        && mv input_dir/sequence.map '$outputmap'
       #end if
     ]]>
   </command>
+  <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" >
+      <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 (--add .)If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved (--seed)">
-          <option value="--add" selected="true" >Yes</option>
-          <option value="--seed">no</option>
+        <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 name="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 name="map" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of positions (--mapout)" 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 name="reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences (--reorder)"  />
+    <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"/>
@@ -63,11 +73,11 @@
   <tests>
     <test expect_num_outputs="1" >
       <param name="inputSequences" value="add_seq.fa"/>
-      <param name="inputAlignment" value="mafft_fftns_result.aln"/>
+      <param name="inputAlignment" value="mafft_default.aln"/>
       <param name="sequenceType" value="singleseq"/>
       <param name="preservegap" value="--add"/>
       <param name="keeplength" value="--keeplength"/>
-      <param name="map" value=""/>
+      <param name="mapout" value=""/>
       <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
     </test>
   </tests>