annotate expression_get_biomaterials.xml @ 0:2dc7f958f3ff draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864

<?xml version="1.0"?>
<tool id="expression_get_biomaterials" name="Chado biomaterial get" 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 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 $biomaterial_name:
  --biomaterial_name '$biomaterial_name'
#end if
#if $analysis_id:
  --analysis_id '$analysis_id'
#end if

| jq -S . > $results
    ]]></command>
	<inputs>
	    <!-- options -->
		<param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
		<param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" optional="true" />
		<param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" optional="true" />
		<param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial id" optional="true" />
		<param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Limit query to the selected biomaterial name" optional="true" />

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

@HELP@
	</help>
</tool>