annotate feature_load_featureprops.xml @ 0:b5d8e6e26d01 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27

<?xml version="1.0"?>
<tool id="feature_load_featureprops" name="Chado load feature properties" 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_featureprops
'$tab_file'
'$analysis_id'
'$organism'
'$prop_type'

#if $feature_type:
  --feature_type '$feature_type'
#end if
#if $match_on_name:
  $match_on_name
#end if

| jq -S . > $results
    ]]></command>
	<inputs>
        <!-- arguments -->
    	<param name="tab_file" label="Tab File" argument="tab_file" type="data" format="tabular" help="Path to the tabular file to load" />
    	<param argument="--analysis_id"
    		type="select"
    		dynamic_options="list_analyses()"
    		label="Analysis" />
        <param argument="--organism"
               type="select"
               dynamic_options="list_organisms()"
               label="Organism" />
    	<param name="prop_type" label="Property type" argument="prop_type" type="text" help="Type of the feature property (cvterm will be created if it doesn't exist)" />

        <!-- options -->
    	<param name="feature_type" label="Feature type" argument="feature_type" type="text" help="Type of the target features in sequence ontology (will speed up loading if specified)" optional="true" />
    	<param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />

        <expand macro="wait_for"/>

	</inputs>
	<outputs>
		<data format="json" name="results"/>
	</outputs>
	<help>
Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)

@HELP@
	</help>
</tool>