<?xml version="1.0"?>
<tool id="feature_load_go" name="Chado load GO annotation" version="@WRAPPER_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <code file="chado.py"/>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
@START_PSQL@ &&

chakin load go
'$input'
'$organism_id'
'$analysis_id'

--query_type '$query_type'

$match_on_name

--name_column '$name_column'
--go_column '$go_column'

#if $re_name:
  --re_name '$re_name'
#end if

$skip_missing

 > '$results'

@ZIP_PSQL@
    ]]></command>
    <inputs>
        <expand macro="psql_target"/>
        <!-- arguments -->
        <param name="input" label="GO annotation" argument="input" type="data" format="tabular" help="Path to the GO annotation file to load" />
        <param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" />
        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />

        <!-- options -->
        <param name="query_type" label="Query type" argument="--query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />

        <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" />

        <param name="name_column" label="Identifier column" argument="--name_column" type="integer" value="2" help="Column containing the feature identifiers." />

        <param name="go_column" label="GO column" argument="--go_column" type="integer" value="5" help="Column containing the GO id." />

        <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
            <expand macro="sanitized"/>
        </param>

        <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features or GO id instead of aborting everything." />

        <expand macro="wait_for"/>
    </inputs>
    <outputs>
        <data format="txt" 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 GO annotation from a tabular file

@HELP@
    </help>
</tool>