annotate instructor.xml @ 0:f93749376fe5 draft

planemo upload for repository https://github.com/brsynth/icfree-ml commit e908694368c306390bc9253f81a9249ad988970d

<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[
        #set sps = []
        #set sws = []
        #set dps = []
        #set dws = []
        #for $x in $plates_generator:
            #set $fname = str($x.element_identifier)
            echo "$fname " &&
            ln -sfn '$x' '$fname' &&
            #if $fname.startswith('source') and $fname.endswith('json'):
                #silent sps.append($fname)
            #else if $fname.startswith('source') and $fname.endswith('tsv'):
                #silent sws.append($fname)
            #else if $fname.startswith('destination') and $fname.endswith('json'):
                #silent dps.append($fname)
            #else if $fname.startswith('destination') and $fname.endswith('tsv'):
                #silent dws.append($fname)
            #end if
        #end for
        #set s_sps = '" "'.join($sps)
        #set s_sws = '" "'.join($sws)
        #set s_dps = '" "'.join($dps)
        #set s_dws = '" "'.join($dws)
        python -m icfree.instructor
            --source_plates $s_sps
            --source_wells $s_sws
            --dest_plates $s_dps
            --dest_wells $s_dws
            -spt '$source_plate'
            --robot '$robot'
            --output-folder '.' &&
        mv instructions.csv '$output_instruction' &&
        #if not os.path.isfile('volume_warning.tsv')
            touch volume_warning.tsv &&
        #end if
        mv volume_warning.tsv '$output_warning'
    ]]></command>
    <inputs>
        <param name="plates_generator" type="data_collection" collection_type="list" format="json,tabular" label="Source/Destination corresponding to plate/wells" help="Output from iCFree plates generator"/>
        <param name="robot" type="select" label="Robot name">
            <option value="ECHO" selected="true">ECHO</option>
        </param>
        <param name="source_plate" type="select" label="Source plate type">
            <option value="384PP_AQ_GP3" selected="true">384PP_AQ_GP3</option>
            <option value="384_AQ_CP">384_AQ_CP</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_warning" format="tsv" label="${tool.name} - Warning" />
        <data name="output_instruction" format="csv" label="${tool.name} - Instruction" />
    </outputs>
    <tests>
        <test>
            <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="plates_generator">
                <collection type="list">
                    <element name="plates_generator_source_plate_1" value="plates_generator_source_plate_1.test-1.json" />
                    <element name="plates_generator_source_plate_1.test-1.tsv" value="plates_generator_source_plate_1.test-1.tsv" />
                    <element name="plates_generator_destination_plate_1.test-1.json" value="plates_generator_destination_plate_1.test-1.json" />
                    <element name="plates_generator_destination_plate_1.test-1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" />
                </collection>
            </param>
            <output name="output_warning" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="12"/>
                    <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
                </assert_contents>
            </output>
            <output name="output_instruction" file="instructor_instructions.csv" ftype="csv" compare="diff" />
        </test>
    </tests>
    <help><![CDATA[
Instructor
==========

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

Input
-----
Required:
* **A collection**: a collection with source/destination plates/wells, coming from iCFree plates generator tool.

Advanced options:
-----------------
* **Robot name**: name of the robot to generate instructions for (default: "ECHO")
* **Source plate type**: type of plate used (default: "384PP_AQ_GP3")

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>