comparison gfastats.xml @ 3:8ccbf07a5433 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5

2:ad1149b4f795

                --nstar-report
            #else
                --seq-report
                $mode_condition.statistics_condition.out_sequence
            #end if
            $mode_condition.tabular > '$stats'
        #else
            --agp-to-path $mode_condition.agp_to_path
            $mode_condition.discover_paths
            -o dataset.gfa
        #end if
        #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding'
            && mv dataset* output_dataset
        #end if
    ]]></command>
    <inputs>

                            <option value="g">Gaps</option>
                        </param>
                    </when>
                    <when value="coordinates">
                        <param argument="--out-coord" type="select" label="BED coordinares feature"
                            help="Generates bed coordinates of given feature. Default: agp">
                            <option value="a">AGP</option>
                            <option value="c">Contigs</option>
                            <option value="g">Gaps</option>
                        </param>
                    </when>

                            label="Report actual sequence" help="It reports also the actual sequence"/>
                    </when>
                </conditional>
                <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
                    label="Tabular-format output" help="Generate output in tabular format"/>
            </when>
            <when value="scaffolding">
                <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" />
                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="generates the initial set of paths" help="In the graph space an assembly 
                    is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
            </when>
        </conditional>
    </inputs>
    <outputs>

                <param name="target_option" value="true"/>
                <param name="include_bed" value="regions.bed"/>
            </conditional>
            <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

3:8ccbf07a5433

                --nstar-report
            #else
                --seq-report
                $mode_condition.statistics_condition.out_sequence
            #end if
            $mode_condition.discover_paths
            $mode_condition.tabular > '$stats'
        #else
            --agp-to-path $mode_condition.agp_to_path
            $mode_condition.discover_paths
            -o dataset.gfa
        #end if
        --threads \${GALAXY_SLOTS:-8}
        #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding'
            && mv dataset* output_dataset
        #end if
    ]]></command>
    <inputs>

                            <option value="g">Gaps</option>
                        </param>
                    </when>
                    <when value="coordinates">
                        <param argument="--out-coord" type="select" label="BED coordinares feature"
                            help="Generates bed coordinates of given feature. Default: AGP">
                            <option value="a">AGP</option>
                            <option value="c">Contigs</option>
                            <option value="g">Gaps</option>
                        </param>
                    </when>

                            label="Report actual sequence" help="It reports also the actual sequence"/>
                    </when>
                </conditional>
                <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
                    label="Tabular-format output" help="Generate output in tabular format"/>
                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly 
                    is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
            </when>
            <when value="scaffolding">
                <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" />
                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly 
                    is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
            </when>
        </conditional>
    </inputs>
    <outputs>

                <param name="target_option" value="true"/>
                <param name="include_bed" value="regions.bed"/>
            </conditional>
            <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>
        </test>
        <!--Test 12 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_04.gfa"/>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="assembly"/>
                </conditional>
                <param name="tabular" value="false"/>
                <param name="discover_paths" value="true"/>
            </conditional>
            <output name="stats" value="test_12_stats.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark