<?xml version="1.0"?>
<tool id="phylogeny_gene_families" name="Chado refresh gene families" version="@WRAPPER_VERSION@.0">
    <description>for phylogeny module</description>
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
	<command detect_errors="aggressive"><![CDATA[
@START_PSQL@ &&

chakin phylogeny gene_families

#if $family_name:
  --family_name '$family_name'
#end if

$nuke

 > '$results'

 && @ZIP_PSQL@
    ]]></command>
	<inputs>
		  <expand macro="psql_target"/>
      <!-- options -->
    	<param name="family_name" label="Family Name" argument="--family_name" type="text" help="Restrict to families beginning with given prefix" />
    	<param name="nuke" label="Nuke" argument="--nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene families 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>
Adds an entry in the featureprop table in a chado database for each family a gene belongs to (for use in https://github.com/legumeinfo/lis_context_viewer/).

@HELP@
	</help>
</tool>