comparison junction_saturation.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

62:473382134e56

    <description>detects splice junctions from each subset and compares them to reference gene model</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <version_command><![CDATA[junction_saturation.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        junction_saturation.py
            --input-file 'input.${extension}'

            --percentile-ceiling ${percentiles_type.upBound}
            --percentile-step ${percentiles_type.percentileStep}
        #end if
        ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <expand macro="refgene_param" />
        <expand macro="min_intron_param" />
        <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)" />
        <expand macro="mapq_param" />
        <conditional name="percentiles_type">
            <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency">
                <option value="default" selected="true">Default sampling bounds and frequency</option>
                <option value="specify">Specify sampling bounds and frequency</option>
            </param>
            <when value="specify">
                <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)">
                    <validator type="in_range" min="0" max="100" />
                </param>
                <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)">
                    <validator type="in_range" min="0" max="100" />
                </param>
                <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)">
                    <validator type="in_range" min="0" max="100" />
                </param>
            </when>
            <when value="default"/>
        </conditional>
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/>
        <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <param name="rscript_output" value="true" />
            <output name="outputr" file="output.junctionSaturation_plot_r" compare="sim_size">
                <assert_contents>
                    <has_line line="pdf('output.junctionSaturation_plot.pdf')" />
                    <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)" />
                </assert_contents>
            </output>
            <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size" />
        </test>
    </tests>

    <help><![CDATA[
junction_saturation.py
++++++++++++++++++++++

It's very important to check if current sequencing depth is deep enough to perform

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>

63:27e16a30667a

    <description>detects splice junctions from each subset and compares them to reference gene model</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA[junction_saturation.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        junction_saturation.py
            --input-file 'input.${extension}'

            --percentile-ceiling ${percentiles_type.upBound}
            --percentile-step ${percentiles_type.percentileStep}
        #end if
        ]]>
    </command>
    <inputs>
        <expand macro="bam_sam_param"/>
        <expand macro="refgene_param"/>
        <expand macro="min_intron_param"/>
        <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)"/>
        <expand macro="mapq_param"/>
        <conditional name="percentiles_type">
            <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency">
                <option value="default" selected="true">Default sampling bounds and frequency</option>
                <option value="specify">Specify sampling bounds and frequency</option>
            </param>
            <when value="specify">
                <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)">
                    <validator type="in_range" min="0" max="100"/>
                </param>
                <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)">
                    <validator type="in_range" min="0" max="100"/>
                </param>
                <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)">
                    <validator type="in_range" min="0" max="100"/>
                </param>
            </when>
            <when value="default"/>
        </conditional>
        <expand macro="rscript_output_param"/>
    </inputs>
    <outputs>
        <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/>
        <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <param name="rscript_output" value="true"/>
            <output name="outputr" file="output.junctionSaturation_plot_r" compare="sim_size">
                <assert_contents>
                    <has_line line="pdf('output.junctionSaturation_plot.pdf')"/>
                    <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)"/>
                </assert_contents>
            </output>
            <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
junction_saturation.py
++++++++++++++++++++++

It's very important to check if current sequencing depth is deep enough to perform

@ABOUT@

]]>
    </help>
    <expand macro="citations"/>
</tool>