--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DNAconvert.xml	Sun Jan 29 16:32:28 2023 +0000
@@ -0,0 +1,184 @@
+<tool id="DNAconvert" name="DNAconvert" version="0.2.0" python_template_version="3.5" profile="21.05">
+    <description>Converts genetic sequences between different formats</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[$__tool_directory__/DNAconvert '$input1' '$output1' '--cmd' 
+          #if $allow_empty_sequences: 
+             --allow_empty_sequence 
+          #end if
+          #if $disable_automatic_renaming: 
+             --disable_automatic_renaming
+          #end if
+            --informat '$informat1'
+	 --outformat '$outformat_and_extension.outformat1' ]]>
+    </command>
+    <inputs>
+        <param  type="data" name="input1" label="Source file" format="data" />
+        <param name="informat1" type="select" label="Input Format">
+           <option value="tab">Internal tab format</option>
+           <option value="tab_noheaders">Internal tab format without headers</option>
+           <option value="fasta">FASTA format</option>
+           <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>
+           <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>
+           <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>
+           <option value="fastq">FASTQ format</option>
+           <option value="phylip">Phylip format</option>
+           <option value="relaxed_phylip">relaxed Phylip format</option>
+           <option value="nexus">NEXUS format</option>
+           <option value="nexml">DnaCharacterMatrix in NeXML format</option>
+           <option value="genbank">Genbank flat file format</option>
+        </param>
+        <conditional name="outformat_and_extension">
+          <param name="outformat1" type="select" label="Output Format">
+             <option value="tab">Internal tab format</option>
+             <option value="tab_noheaders">Internal tab format without headers</option>
+             <option value="fasta">FASTA format</option>
+             <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>
+             <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>
+             <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>
+             <option value="fastq">FASTQ format</option>
+             <option value="phylip">Phylip format</option>
+             <option value="relaxed_phylip">relaxed Phylip format</option>
+             <option value="nexus">NEXUS format</option>
+             <option value="nexml">DnaCharacterMatrix in NeXML format</option>
+             <option value="genbank">Genbank flat file format</option>
+          </param>
+          <when value="tab">
+            <param name="extension1" type="hidden" value="tab"/>
+          </when>
+          <when value="phylip">
+            <param name="extension1" type="hidden" value="phy"/>
+          </when>
+          <when value="fasta">
+            <param name="extension1" type="hidden" value="fas"/>
+          </when>
+          <when value="fasta_hapview">
+            <param name="extension1" type="hidden" value="fas"/>
+          </when>
+          <when value="fasta_gbexport">
+            <param name="extension1" type="hidden" value="fas"/>
+          </when>
+          <when value="mold_fasta">
+            <param name="extension1" type="hidden" value="fas"/>
+          </when>
+          <when value="fastq">
+            <param name="extension1" type="hidden" value="fq"/>
+          </when>
+          <when value="tab_noheaders">
+            <param name="extension1" type="hidden" value="tab"/>
+          </when>
+          <when value="relaxed_phylip">
+            <param name="extension1" type="hidden" value="phy"/>
+          </when>
+          <when value="nexus">
+            <param name="extension1" type="hidden" value="nex"/>
+          </when>
+          <when value="nexml">
+            <param name="extension1" type="hidden" value="xml"/>
+          </when>
+          <when value="genbank">
+            <param name="extension1" type="hidden" value="gb"/>
+          </when>
+        </conditional>          
+
+        <param name="allow_empty_sequences" type="boolean" label="Allow empty sequences"  help="set this to keep the empty sequences in the output file" />
+        <param name="disable_automatic_renaming" type="boolean" label="Disable automatic renaming"  help="disables automatic renaming, may result in duplicate sequence names in Phylip and Nexus files" />
+    </inputs>
+    <outputs>
+        <data name="output1" label="${os.path.splitext(os.path.basename($input1.name))[0]}.${outformat_and_extension.extension1}"  metadata_source="input1" format="tabular">
+           <change_format>
+              <when input="outformat_and_extension.outformat1" value="phylip" format="phylip" />
+              <when input="outformat_and_extension.outformat1" value="fasta" format="fasta" />
+              <when input="outformat_and_extension.outformat1" value="tab_noheaders" format="tabular" />
+              <when input="outformat_and_extension.outformat1" value="tab" format="tabular" />
+              <when input="outformat_and_extension.outformat1" value="fasta_hapview" format="fasta" />
+              <when input="outformat_and_extension.outformat1" value="fastq" format="fastq" />
+              <when input="outformat_and_extension.outformat1" value="relaxed_phylip" format="phylip" />
+              <when input="outformat_and_extension.outformat1" value="nexus" format="nexus" />
+              <when input="outformat_and_extension.outformat1" value="nexml" format="nexml" />
+              <when input="outformat_and_extension.outformat1" value="genbank" format="gb" />
+              <when input="outformat_and_extension.outformat1" value="mold_fasta" format="fasta" />
+           </change_format>
+        </data>
+    </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="DNAconvert_examplefile2_iTaxoTools_0_1.fas"/>
+      <param name="informat1" value="fasta" />
+      <param name="outformat1" value="tab" />
+      <output name="output1" file="DNAtestout_1.tab"/>
+    </test>
+    <test>
+      <param name="input1" value="DNAconvert_examplefile3_iTaxoTools_0_1.tab"/>
+      <param name="informat1" value="tab" />
+      <param name="outformat1" value="phylip" />
+      <output name="output1" file="DNAtestout_2.phy"/>
+    </test>
+  </tests> 
+    <help><![CDATA[
+
+**DNAconvert**
+
+A program to convert between different file formats containing DNA sequences. 
+Written by V. Kharchev in the framework of the iTaxoTools project.
+Galaxy wrapper for DNAconvert 0.1 written in 2022/2023 by F. Fischell.
+
+Standalone executables with graphical user interface of the newest version of ASAP for Windows and Mac are available from:
+
+http://itaxotools.org/
+
+https://github.com/iTaxoTools/iTaxoTools-Executables/releases
+
+
+For more information, see the iTaxoTools manual available at:
+http://itaxotools.org/
+
+**Usage**
+
+- Specify an input file and the input file format, as well as the desired output file format. 
+- DNAconvert will "sanitize" sequence names by replacing special characters by underscores
+- For formats that require unique sequence names, DNAconvert can automatically rename sequnces by adding consecutive numbers to the names
+- An important feature of DNAconvert is the option to use tab-delimited files which allows curating sequence data sets with metadata in spreadsheet editors. Refer to the iTaxoTool manual for details.
+
+**Supported formats**
+
+* `tab` = tsv: [Internal tab format][1]  = tab-delimited text
+
+* `tab_noheaders`: [Internal tab format][1] without headers  = tab-delimited text without headers
+
+* `fasta`: FASTA format
+
+* `phylip`: Phylip format
+
+* `relaxed_phylip`: relaxed Phylip format (with no restriction on the length of sequence names)
+
+* `fasta_hapview`: FASTA format with sequence names formatted for Haplotype Viewer
+
+* `fastq`: FASTQ format
+
+* `fasta_gbexport`: FASTA format with sequence names adjusted for export into GenBank repository
+
+* `nexus`: NEXUS format
+
+* `nexml`: DnaCharacterMatrix in NeXML format
+
+* `genbank`: Genbank flat file format
+
+* `mold_fasta`: FASTA format with sequence name matching requirements for the tool MolD *
+
+
+**Recognised extension**
+
+Automatic recognition of file format based on extension in file name not yet available in the Galaxy implementation. 
+
+
+
+
+
+    ]]></help>
+    <citations>
+	<citation type="doi">
+	    10.11646/megataxa.6.2.1 
+	</citation>
+    </citations>
+</tool>