<?xml version="1.0"?>
<tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0">
    <description>for phylogeny module</description>
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
    <code file="chado.py"/>
	<command detect_errors="aggressive"><![CDATA[
@AUTH@

#if $input.input_type == "archive":
	mkdir 'newick_arch/' &&
	tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
#end if

chakin phylogeny load_tree

$match_on_name

#if $prefix:
  --prefix '$prefix'
#end if

#if $xref_db:
  --xref_db '$xref_db'
#end if

#if $input.input_type == "archive":
	#if $name:
	  --name '$name'
	#end if

	#if $xref_accession:
	  --xref_accession '$xref_accession'
	#end if

	'$newick'
#else
	'newick_arch/'
#end if

'$analysis_id'

| jq -S . > '$results'
    ]]></command>
	<inputs>
		<param argument="analysis_id"
			type="select"
			dynamic_options="list_analyses()"
			label="Analysis" />

        <conditional name="input">
            <param name="input_type" type="select" label="Input type">
                <option value="file" selected="true">Newick file</option>
                <option value="archive">Tar.gz archive of Newick files</option>
            </param>
            <when value="file">
				<param name="newick" label="Newick" argument="newick" type="data" format="newick" help="Newick file to load" />
				<param name="name" label="Name" argument="--name" type="text" help="The name given to the phylotree entry in the database" />
				<param name="xref_accession" label="Xref Accession" argument="--xref_accession" type="text" help="The accession to use for dbxrefs for the trees (assumed same as name unless otherwise specified)" />
			</when>
            <when value="archive">
				<param name="newick_arch" label="Newicks archive" type="data" format="tar" help="Archive of Newick files to load (must be at the root of the archive)" />
			</when>
		</conditional>

	    <!-- options -->
		<param name="xref_db" label="Xref db" argument="--xref_db" value="null" type="text" help="The name of the db to link dbxrefs for the trees" />
		<param name="match_on_name" label="Match On Name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match polypeptide features using their name instead of their uniquename" />
		<param name="prefix" label="Prefix" argument="--prefix" type="text" help="Comma-separated list of prefix to be removed from identifiers (e.g species prefixes when loading OrthoFinder output)" />
		<expand macro="wait_for"/>

	</inputs>
	<outputs>
		<data format="json" name="results"/>
	</outputs>
	<help>
Load a phylogenetic tree (Newick format) into Chado db

@HELP@
	</help>
</tool>