<tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
    <description>Generates a list of Echo-compatible instructions to prepare samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command detect_errors="exit_code"><![CDATA[
        #if str($conditional_source_json.type) == "collection":
            #for $input in $conditional_source_json.collection.keys():
                ln -sfn $conditional_source_json.collection[$input] '.' &&
            #end for
            #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.collection[$input]])
        #elif str($conditional_source_json.type) == "files":
            #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.files])
        #end if

        #if str($conditional_source_tsv.type) == "collection":
            #for $input in $conditional_source_tsv.collection.keys():
                ln -sfn $conditional_source_tsv.collection[$input] '.' &&
            #end for
            #set input_source_tsv = '" "'.join([str($file) for $file in $conditional_source_tsv.collection[$input]])
        #elif str($conditional_source_tsv.type) == "files":
            #set input_source_tsv = []
            #for $f in $conditional_source_tsv.files
                ln -sfn '$f' '$f.element_identifier' &&
                #silent input_source_tsv.append(str($f.element_identifier))
            #end for
            #set inputs_source_tsv = '" "'.join(input_source_tsv)
        #end if


        #if str($conditional_destination_json.type) == "collection":
            #for $input in $conditional_destination_json.collection.keys():
                ln -sfn $conditional_destination_json.collection[$input] '.' &&
            #end for
            #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.collection[$input]])
        #elif str($conditional_destination_json.type) == "files":
            #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.files])
        #end if

        #if str($conditional_destination_tsv.type) == "collection":
            #for $input in $conditional_destination_tsv.collection.keys():
                ln -sfn $conditional_destination_tsv.collection[$input] '.' &&
            #end for
            #set input_destination_tsv = '" "'.join([str($file) for $file in $conditional_destination_tsv.collection[$input]])
        #elif str($conditional_destination_tsv.type) == "files":
            #set input_destination_tsv = []
            #for $f in $conditional_destination_tsv.files
                ln -sfn '$f' '$f.element_identifier' &&
                #silent input_destination_tsv.append(str($f.element_identifier))
            #end for
            #set inputs_destination_tsv = '" "'.join(input_destination_tsv)
        #end if


        python -m icfree.instructor
            --source_plates "${input_source_json}"
            --source_wells "${inputs_source_tsv}"
            --dest_plates "${input_destination_json}"
            --dest_wells "${inputs_destination_tsv}"
            --robot '$adv.robot'
            --output-folder out
    ]]></command>
    <inputs>
        <conditional name="conditional_source_json">
            <param name="type" type="select" label="Source plate (json)">
                <option value="files" selected="True">File(s)</option>
                <option value="collection">Collection</option>
            </param>
            <when value="files">
                <param name="files" type="data" format="json" multiple="true" label="Source plates information (json)" />
            </when>
            <when value="collection">
                <param name="collection" type="data_collection" collection_type="list" format="json" label="Source plates information (json)" />
            </when>
        </conditional>
        <conditional name="conditional_source_tsv">
            <param name="type" type="select" label="Source plate (tsv)">
                <option value="files" selected="True">File(s)</option>
                <option value="collection">Collection</option>
            </param>
            <when value="files">
                <param name="files" type="data" format="tabular" multiple="true" label="Source plates information (tsv)" />
            </when>
            <when value="collection">
                <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Source plates information (tsv)" />
            </when>
        </conditional>
        <conditional name="conditional_destination_json">
            <param name="type" type="select" label="Source plate (json)">
                <option value="files" selected="True">File(s)</option>
                <option value="collection">Collection</option>
            </param>
            <when value="files">
                <param name="files" type="data" format="json" multiple="true" label="Destination plates information (json)" />
            </when>
            <when value="collection">
                <param name="collection" type="data_collection" collection_type="list" format="json" label="Destination plates information (json)" />
            </when>
        </conditional>
        <conditional name="conditional_destination_tsv">
            <param name="type" type="select" label="Source plate (tsv)">
                <option value="files" selected="True">File(s)</option>
                <option value="collection">Collection</option>
            </param>
            <when value="files">
                <param name="files" type="data" format="tabular" multiple="true" label="Destination plates information (tsv)" />
            </when>
            <when value="collection">
                <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Destination plates information (tsv)" />
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="robot" type="text" value="echo" label="Robot name" />
        </section>
    </inputs>
    <outputs>
        <data name="tabulars" format="tabular">
            <discover_datasets pattern="__designation__" ext="tabular" directory="out" />
        </data>
    </outputs>
    <tests>
        <test>
            <!-- test 1: check if identical outputs are produced with default parameters  -->
            <conditional name="conditional_source_json">
                <param name="type" value="files"/>
                <param name="files" value="plates_generator_source_plate_1.json" />
            </conditional>
            <conditional name="conditional_source_tsv">
                <param name="type" value="files"/>
                <param name="files" value="plates_generator_source_plate_1.tsv" />
            </conditional>
            <conditional name="conditional_destination_json">
                <param name="type" value="files"/>
                <param name="files" value="plates_generator_destination_plate_1.json" />
            </conditional>
            <conditional name="conditional_destination_tsv">
                <param name="type" value="files"/>
                <param name="files" value="plates_generator_destination_plate_1.tsv" />
            </conditional>
            <output name="tabulars" ftype="tabular">
                <discovered_dataset designation="volumes_warnings.tsv" ftype="tabular">
                    <assert_contents>
                        <has_n_lines n="12"/>
                        <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
                    </assert_contents>
                </discovered_dataset>
                <discovered_dataset designation="instructions.csv" ftype="tabular">
                    <assert_contents>
                        <has_line_matching expression="^Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID$"/>
                        <has_n_lines n="1701"/>
                    </assert_contents>

                </discovered_dataset>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Instructor
==========

The module generates a list of instructions to perform the experiment.

Input
-----
Required:
* **Source plates file**: description of the source plates (source well name, source well volume...) (JSON format)
* **Destination plates file**: description of the destination plates (destination well name, destination well volume...) (JSON format)

Advanced options:
-----------------
* **Robot name**: name of the robot to generate instructions for (default: "echo")

Output
------
* **instructions**: contains the instructions to perform the experiment
* **volumes_warning**: contains the volumes that may cause issues with the chosen robot
    ]]></help>
    <expand macro="creator"/>
    <expand macro="citation"/>
</tool>