<?xml version="1.0"?>
<tool id="expression_add_expression" name="Load expression data" version="@WRAPPER_VERSION@.1">
 <description>into Tripal</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <code file="tripal.py"/>
    <command detect_errors="aggressive"><![CDATA[
tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"

&&

cp '${file_path}' "\${tmp_dir}/expression.tsv"

&&

@AUTH@

tripaille expression add_expression
'$organism_id'
'$analysis_id'
"\${tmp_dir}/expression.tsv"

#if $match_type:
  --match_type '$match_type'
#end if
#if $biomaterial_provider:
  --biomaterial_provider '$biomaterial_provider'
#end if
#if $array_design:
  --array_design '$array_design'
#end if
#if $assay_id:
  --assay_id '$assay_id'
#end if
#if $acquisition_id:
  --acquisition_id '$acquisition_id'
#end if
#if $quantification_id:
  --quantification_id '$quantification_id'
#end if
#if $start_regex:
  --start_regex '$start_regex'
#end if
#if $stop_regex:
  --stop_regex '$stop_regex'
#end if

&&

echo "Data loaded" > '$results'
]]></command>
    <inputs>
        <!-- arguments -->
        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
        <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
        <param name="file_path" label="Expression matrix" argument="file_path" type="data" format="tsv,tabular" help="Expression matric (tabular, rows are transcripts, columns are conditions)" />

        <!-- options -->
        <expand macro="match_type" />

        <param name="biomaterial_provider" label="Biomaterial Provider" argument="biomaterial_provider" type="text" help="The contact who provided the biomaterial. (optional, non functional in Tripal2)" optional="true" />

        <param name="array_design" label="Array Design" argument="array_design" type="text" help="The array design associated with this analysis. This is not required if the experimental data was gathered from next generation sequencing methods. (optional, non functional in Tripal2)" optional="true" />

        <param name="assay_id" label="Assay Id" argument="assay_id" type="text" help="The id of the assay associated with the experiment. (optional, non functional in Tripal2)" optional="true" />

        <param name="acquisition_id" label="Acquisition Id" argument="acquisition_id" type="text" help="The id of the acquisition associated with the experiment (optional, non functional in Tripal2)" optional="true" />

        <param name="quantification_id" label="Quantification Id" argument="quantification_id" type="text" help="The id of the quantification associated with the experiment (optional, non functional in Tripal2)" optional="true" />

        <param name="start_regex" label="Start Regex" argument="start_regex" type="text" help="A regular expression to describe the line that occurs before the start of the expression data. If the file has no header, this is not needed. (optional)">
            <expand macro="sanitized"/>
        </param>

        <param name="stop_regex" label="Stop Regex" argument="stop_regex" type="text" help="A regular expression to describe the line that occurs after the end of the expression data. If the file has no footer text, this is not needed. (optional)">
            <expand macro="sanitized"/>
        </param>

        <expand macro="wait_for"/>

    </inputs>
    <outputs>
        <data format="txt" name="results"/>
    </outputs>
    <help>
:type organism_id: str :param organism_id: Organism Id

@HELP@
    </help>
</tool>