<?xml version="1.0"?>
<tool id="expression_get_biomaterials" name="Get biomaterials" version="@WRAPPER_VERSION@.0">
 <description>from Tripal</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.5">jq</requirement>
    </expand>
    <code file="tripal.py"/>
    <command detect_errors="aggressive"><![CDATA[
@AUTH@

tripaille expression get_biomaterials

#if $provider_id:
  --provider_id '$provider_id'
#end if
#if $biomaterial_id:
  --biomaterial_id '$biomaterial_id'
#end if
#if $organism_id:
  --organism_id '$organism_id'
#end if
#if $dbxref_id:
  --dbxref_id '$dbxref_id'
#end if

| jq -S . > $results
]]></command>
    <inputs>
        <!-- arguments -->

        <!-- options -->
        <param argument="--organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
        <param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" />
        <param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial" />
        <param name="dbxref_id" label="Dbxref Id" argument="dbxref_id" type="text" help="Limit query to the selected ref" />

    </inputs>
    <outputs>
        <data format="json" name="results"/>
    </outputs>
    <help>
List biomaterials in the database

@HELP@
    </help>
</tool>