Mercurial > repos > gga > chado_feature_load_featureprops

<?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[
@START_PSQL@ &&

chakin feature load_featureprops
'$tab_file'
'$analysis_id'
'$organism'
'$prop_type'

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

$match_on_name

| jq -S . > '$results'

&& @ZIP_PSQL@
    ]]></command>
    <inputs>
        <expand macro="psql_target"/>
        <!-- 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"/>
        <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>
Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)

@HELP@
    </help>
</tool>
author	gga
date	Mon, 08 Jul 2019 05:36:34 -0400
parents	46b3ccaa24ca
children	23550bf28405