<?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@

chakin phylogeny load_tree
'$newick'
'$analysis_id'

#if $name:
  --name '$name'
#end if
#if $xref_db:
  --xref_db '$xref_db'
#end if
#if $xref_accession:
  --xref_accession '$xref_accession'
#end if
#if $match_on_name:
  $match_on_name
#end if
#if $prefix:
  --prefix '$prefix'
#end if

| jq -S . > $results
    ]]></command>
	<inputs>
	    <!-- arguments -->
		<param name="newick" label="Newick" argument="newick" type="data" format="txt" help="Newick file to load (or directory containing multiple newick files to load)" />
		<param argument="--analysis_id"
			type="select"
			dynamic_options="list_analyses()"
			label="Analysis" />

	    <!-- options -->
		<param name="name" label="Name" argument="name" type="text" help="The name given to the phylotree entry in the database" />
		<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="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)" />
		<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>