diff mafft-add.xml @ 16:8e649f27aa0d draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443

--- 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>