comparison merqury.xml @ 4:09c589057ee8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4

3:f8113c25bc6b

            <option value="plots" selected="true">Plots</option>
            <option value="sizes">Size files</option>
            <option value="stats" selected="true">Stats file</option>
            <option value="bed">BED: hap-mer tracks</option>
            <option value="wig">WIG: hap-mer tracks</option>
            <option value="log">Log file</option>
        </param>
        <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" />
    </inputs>
    <outputs>

            <filter>"stats" in output_selector</filter>
        </collection>
        <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file">
            <filter>"log" in output_selector</filter>
        </data>
    </outputs>
    <tests>
        <!--Test 01: trio mode-->
        <test expect_num_outputs="1">
            <conditional name="mode">

            <output_collection name="sizes_files" type="list" count="2">
                <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <!--Test 02: standard mode with tabular headers -->
        <test expect_num_outputs="6">
            <conditional name="mode">
                <param name="options" value="default"/>
                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
                <conditional name="assembly_options">
                    <param name="number_assemblies" value="one"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_02"/>
            <param name="output_selector" value="stats,plots,bed,sizes,qv,wig"/>
            <output_collection name="png_files" type="list" count="6">
                <element name="output_02.assembly.spectra-cn.fl">
                    <assert_contents>
                        <has_size value="71874" delta="100"/>
                    </assert_contents>

                    <assert_contents>
                        <has_size value="0"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!--Test 03: Standard mode two assemblies-->
        <test expect_num_outputs="2">
            <conditional name="mode">
                <param name="options" value="default"/>

4:09c589057ee8

            <option value="plots" selected="true">Plots</option>
            <option value="sizes">Size files</option>
            <option value="stats" selected="true">Stats file</option>
            <option value="bed">BED: hap-mer tracks</option>
            <option value="wig">WIG: hap-mer tracks</option>
            <option value="hist">Histogram files</option>
            <option value="log">Log file</option>
        </param>
        <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" />
    </inputs>
    <outputs>

            <filter>"stats" in output_selector</filter>
        </collection>
        <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file">
            <filter>"log" in output_selector</filter>
        </data>
        <collection name="hist_files" type="list" label="${tool.name} on ${on_string}: histograms">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.hist" format="tabular" directory="output_files"/>
            <filter>"hist" in output_selector</filter>
        </collection>
    </outputs>
    <tests>
        <!--Test 01: trio mode-->
        <test expect_num_outputs="1">
            <conditional name="mode">

            <output_collection name="sizes_files" type="list" count="2">
                <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <!--Test 02: standard mode with tabular headers -->
        <test expect_num_outputs="7">
            <conditional name="mode">
                <param name="options" value="default"/>
                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
                <conditional name="assembly_options">
                    <param name="number_assemblies" value="one"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_02"/>
            <param name="output_selector" value="stats,plots,bed,sizes,qv,wig,hist"/>
            <output_collection name="png_files" type="list" count="6">
                <element name="output_02.assembly.spectra-cn.fl">
                    <assert_contents>
                        <has_size value="71874" delta="100"/>
                    </assert_contents>

                    <assert_contents>
                        <has_size value="0"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="hist_files" type="list" count="4">
                <element name="output_02.spectra-asm" file="output_02.spectra-asm.hist" ftype="tabular"/>
                <element name="output_02.dist_only" file="output_02.dist_only.hist" ftype="tabular"/>
                <element name="output_02.assembly.spectra-cn" file="output_02.assembly.spectra-cn.hist" ftype="tabular"/>
                <element name="output_02.assembly.only" file="output_02.assembly.only.hist" ftype="tabular"/>
            </output_collection>
        </test>
        <!--Test 03: Standard mode two assemblies-->
        <test expect_num_outputs="2">
            <conditional name="mode">
                <param name="options" value="default"/>