comparison draw_amr_matrix.xml @ 9:70073df30a06 draft

Uploaded

8:7fe8ea50a81d

    --mutation_regions_dir 'mutation_regions_dir'
#end if
--amr_gene_drug_file '$amr_gene_drug_file'
--reference_genome reference.fa
--amr_matrix_png_dir 'amr_matrix_png_dir'
#if str($output_process_log) == 'yes':
    && mv 'process_log' '$process_log'
#end if
]]></command>
    <inputs>

    </inputs>
    <outputs>
        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
            <filter>output_process_log == 'yes'</filter>
        </data>
        <collection name="mutation_regions_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (mutation regions)">
            <filter>amr_mutation_regions_bed_file not in [None, 'None']</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;tsv)" directory="mutation_regions_dir"/>
        </collection>
        <collection name="amr_matrix_png" type="list" format="png">

                    <assert_contents>
                        <has_size value="25383" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help>
**What it does**

9:70073df30a06

    --mutation_regions_dir 'mutation_regions_dir'
#end if
--amr_gene_drug_file '$amr_gene_drug_file'
--reference_genome reference.fa
--amr_matrix_png_dir 'amr_matrix_png_dir'
--errors '$errors'
#if str($output_process_log) == 'yes':
    && mv 'process_log' '$process_log'
#end if
]]></command>
    <inputs>

    </inputs>
    <outputs>
        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
            <filter>output_process_log == 'yes'</filter>
        </data>
        <data name="errors" format="txt" label="${tool.name} on ${on_string} (errors)"/>
        <collection name="mutation_regions_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (mutation regions)">
            <filter>amr_mutation_regions_bed_file not in [None, 'None']</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;tsv)" directory="mutation_regions_dir"/>
        </collection>
        <collection name="amr_matrix_png" type="list" format="png">

                    <assert_contents>
                        <has_size value="25383" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="errors" value="errors.txt" ftype="txt"/>
        </test>
    </tests>
    <help>
**What it does**