annotate extractor.xml @ 9:2b46c8d5952e draft default tip

planemo upload for repository https://github.com/brsynth/icfree-ml commit 16315dee62caf50b1820964b0536c1cf61c67ceb

<tool id="icfree_extractor" name="iCFree extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT">
    <description>Process fluorescence data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        cp '$initial_data_file' 'initial_data.csv' &&
        cp '$sampling_file' 'sampling.csv' &&
        python -m icfree.learner.extractor
            --initial_data_file 'initial_data.csv'
            --sampling_file 'sampling.csv'
            --output_file 'extractor.csv'
            #if str($adv.num_samples) != ''
                --num_samples '$adv.num_samples'
            #end if
            #if str($adv.num_replicates) != ''
                --num_replicates '$adv.num_replicates'
            #end if
            &&
        mv 'extractor.csv' '$output'
    ]]></command>
    <inputs>
        <param name="initial_data_file" type="data" format="csv" label="FLuo/Lumi values"/>
        <param name="sampling_file" type="data" format="csv" label="Sampling file"/>
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="num_samples" type="integer" optional="true" label="Number of samples" />
            <param argument="num_replicates" type="integer" optional="true" label="Number of replicates" />
        </section>
    </inputs>
    <outputs>
        <data name="output" format="csv" label="${tool.name}" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <!-- python -m icfree.learner.extractor -initial_data_file extractor.input.initial_data.csv -sampling_file extractor.input.sampling.csv -output_file extractor.output.1.csv -->
            <param name="initial_data_file" value="extractor.input.initial_data.csv" />
            <param name="sampling_file" value="extractor.input.sampling.csv" />
            <output name="output" ftype="csv">
                <assert_contents>
                    <has_n_lines n="58" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- python -m icfree.learner.extractor -initial_data_file extractor.input.initial_data.csv -sampling_file extractor.input.sampling.csv -output_file extractor.output.2.csv -num_samples 20 -num_replicates 3 -->
            <param name="initial_data_file" value="extractor.input.initial_data.csv" />
            <param name="sampling_file" value="extractor.input.sampling.csv" />
            <param name="num_samples" value="20" />
            <param name="num_replicates" value="3" />
            <output name="output" ftype="csv">
                <assert_contents>
                    <has_n_lines n="21" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Extractor
==========
Process fluoresence data

]]></help>
    <expand macro="creator"/>
    <expand macro="citation"/>
</tool>