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

chakin feature load_fasta
'$fasta'
'$organism'

#if $sequence_type:
  --sequence_type '$sequence_type'
#end if
#if $analysis_id:
  --analysis_id '$analysis_id'
#end if
#if $re_name:
  --re_name '$re_name'
#end if
#if $re_uniquename:
  --re_uniquename '$re_uniquename'
#end if
#if $match_on_name:
  $match_on_name
#end if
#if $update:
  $update
#end if
#if $ext_db.db:
  --db '${ext_db.db}'
#end if
#if $ext_db.re_db_accession:
  --re_db_accession '${ext_db.re_db_accession}'
#end if

#if str($relationships.rel_type) != "none":
    --rel_type '${relationships.rel_type}'
    --re_parent '${relationships.rel_subject_re}'
    --parent_type '${relationships.rel_subject_type}'
#end if

| jq -S . > $results
    ]]></command>
	<inputs>
	    <!-- arguments -->
		<param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" />
	    <param argument="--organism"
	           type="select"
	           dynamic_options="list_organisms()"
	           label="Organism" />

	    <!-- options -->
		<param argument="--analysis_id"
			type="select"
			dynamic_options="list_analyses()"
			label="Analysis" />
		<param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/>

		<param name="re_name" label="Name regular expression" argument="re_name" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" />
		<param name="re_uniquename" label="Uniquename regular expression" argument="re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" />
		<param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" />
		<param name="update" label="Update" argument="update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" />
	    <conditional name="relationships">
			<param name="rel_type"
				   argument="--rel_type"
				   type="select"
				   label="Relationship type"
				   help="Use this when inserting features that should be associated to other already existing features">
				<option value="none" selected="true">No relationship</option>
				<option value="part_of">Part of (for CDS sequences)</option>
				<option value="derives_from">Derives from (for peptide sequences)</option>
			</param>
			<when value="none"/>
			<when value="part_of">
				<expand macro="feature_rel" />
			</when>
			<when value="derives_from">
				<expand macro="feature_rel" />
			</when>
		</conditional>
	    <section name="ext_db" title="Cross references to external database">
			<param name="db" label="Db" argument="db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db -->
			<param name="re_db_accession" label="Regex external db accession" argument="re_db_accession" type="text" help="Regular expression to extract an external database accession from the fasta sequence id (first capturing group will be used)." optional="true" />
	    </section>
	    <expand macro="wait_for"/>
	</inputs>
	<outputs>
		<data format="json" name="results"/>
	</outputs>
	<help>
Load features from a fasta file

@HELP@
	</help>
</tool>