<tool id="pcdl_get_conc_df" name="pcdl_get_conc_df" version="3.0.1+galaxy0" profile="21.05">
    <macros>
        <import>pcdl_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement"/>
    </requirements>
    <command><![CDATA[
        #import re
        mkdir output_pc &&
        #for $file in $path:
            #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
            ln -s '$file' output_pc/$filename &&
        #end for

        pcdl_get_conc_df 'output_pc' $entropy
        --verbose $verbose
        --drop $drop
        --keep $keep
        --collapse $collapse
    ]]></command>
    <inputs>
        <section name="essential" title="essential:" expanded="true">
            <expand macro="path"/>
            <expand macro="entropy"/>
            <expand macro="drop"/>
            <expand macro="keep"/>
            <expand macro="collapse"/>
        </section>
        <section name="advanced" title="advanced:" expanded="false">
            <expand macro="verbose"/>
        </section>
    </inputs>
    <outputs>
        <collection name="conc_csv" type="list">
            <discover_datasets pattern="(?P&lt;designation&gt;.+_conc)\.csv" format="csv" directory="output_pc" visible="false"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <section name="essential">
                <param name="path">
                    <expand macro="output"/>
                </param>
                <param name="collapse" value="true"/>
            </section>
            <section name="advanced">
                <param name="verbose" value="true"/>
            </section>
            <output_collection name="conc_csv" count="1">
                <element name="timeseries_conc">
                    <assert_contents>
                        <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p"/>
                        <has_text text=",time,runtime,xmlfile"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <section name="essential">
                <param name="path">
                    <expand macro="output"/>
                </param>
                <param name="collapse" value="false"/>
            </section>
            <section name="advanced">
                <param name="verbose" value="false"/>
            </section>
            <output_collection name="conc_csv" count="2">
                <element name="output00000000_conc">
                    <assert_contents>
                        <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
                        <has_text text=",time,runtime,xmlfile"/>
                    </assert_contents>
                </element>
                <element name="output00000001_conc">
                    <assert_contents>
                        <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
                        <has_text text=",time,runtime,xmlfile"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
This function extracts dataframes with concentration values for all chemical species in all voxels and saves them as csv files. Additionally, this dataframe lists voxel and mesh center coordinates.

Homepage: https://github.com/elmbeech/physicelldataloader
    ]]></help>
    <citations>
        <expand macro="citation"/>
    </citations>
</tool>