comparison draw_amr_matrix.xml @ 13:b1a7e04e6371 draft

Uploaded

12:aa2b737102dc

--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>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?">
                <option value="cached">Use a cached genome index</option>

        <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/>
        <param name="output_process_log" type="select" display="radio" label="Output process log file?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
            <filter>output_process_log == 'yes'</filter>
        </data>

                </collection>
            </param>
            <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/>
            <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/>
            <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/>
            <output_collection name="amr_matrix_png" type="list" count="1">
                <element name="amr_matrix" ftype="png">
                    <assert_contents>
                        <has_size value="28798" delta="1000"/>
                    </assert_contents>

13:b1a7e04e6371

--amr_matrix_png_dir 'amr_matrix_png_dir'
--errors '$errors'
#if str($output_process_log) == 'yes':
    && mv 'process_log' '$process_log'
#end if
--in_test_mode '$in_test_mode'
]]></command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?">
                <option value="cached">Use a cached genome index</option>

        <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/>
        <param name="output_process_log" type="select" display="radio" label="Output process log file?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="in_test_mode" type="hidden" value="false"/>
    </inputs>
    <outputs>
        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
            <filter>output_process_log == 'yes'</filter>
        </data>

                </collection>
            </param>
            <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/>
            <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/>
            <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/>
            <param name="in_test_mode" value="true"/>
            <output_collection name="amr_matrix_png" type="list" count="1">
                <element name="amr_matrix" ftype="png">
                    <assert_contents>
                        <has_size value="28798" delta="1000"/>
                    </assert_contents>