<?xml version="1.0"?>
<tool id="phylogeny_gene_order" name="Chado gene ordering" version="@WRAPPER_VERSION@">
 	<description>for phylogeny module</description>
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
	<command detect_errors="aggressive"><![CDATA[
@START_PSQL@ &&

chakin phylogeny gene_order

$nuke

 > '$results'

 @ZIP_PSQL@
    ]]></command>
	<inputs>
		<expand macro="psql_target"/>
    <!-- options -->
		<param name="nuke" label="Nuke" argument="--nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene ordering data" />
	    <expand macro="wait_for"/>

	</inputs>
	<outputs>
		<data format="txt" name="results"/>
    <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
      <filter>psql_target['method'] == "pgtools"</filter>
    </data>
	</outputs>
	<help>
Orders all the genes in the database by their order on their respective chromosomes in the gene_order table (for use in https://github.com/legumeinfo/lis_context_viewer/).

@HELP@
	</help>
</tool>