comparison scatter.xml @ 1:3323a7867128 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22

0:ec9731970f8b

    <description>Plot bin-level log2 coverages and segmentation calls together</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_cnr_file' ./tumor.cnr &&
        #if $advanced_settings.segment
        ln -s '$advanced_settings.segment' ./segment.cns &&

        #if $advanced_settings.additional_SNP_allelic_process.vcf
            ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
        #end if
        cnvkit.py scatter
            ./tumor.cnr
            --output sample-scatter.png
            #if $advanced_settings.segment
                --segment ./segment.cns
            #end if
            #if $advanced_settings.chromosome
                --chromosome '$advanced_settings.chromosome'

            #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
                --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
            #end if
    ]]></command>
    <inputs>
        <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <expand macro="scatter_optional" />
            <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
              <expand macro="scatter_plot" />
            </section>

              <expand macro="additionally_SNP_process" />
            </section>
        </section>   
    </inputs>
    <outputs>
        <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
            <param name="zygosity_freq" value="0.25" />
            <param name="by_bin" value="1" />
            <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size">
                <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

1:3323a7867128

    <description>Plot bin-level log2 coverages and segmentation calls together</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_cnr_file' ./tumor.cnr &&
        #if $advanced_settings.segment
        ln -s '$advanced_settings.segment' ./segment.cns &&

        #if $advanced_settings.additional_SNP_allelic_process.vcf
            ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
        #end if
        cnvkit.py scatter
            ./tumor.cnr
            --output sample-scatter.pdf
            #if $advanced_settings.segment
                --segment ./segment.cns
            #end if
            #if $advanced_settings.chromosome
                --chromosome '$advanced_settings.chromosome'

            #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
                --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
            #end if
    ]]></command>
    <inputs>
        <param name="input_cnr_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <expand macro="scatter_optional" />
            <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
              <expand macro="scatter_plot" />
            </section>

              <expand macro="additionally_SNP_process" />
            </section>
        </section>   
    </inputs>
    <outputs>
        <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
            <param name="zygosity_freq" value="0.25" />
            <param name="by_bin" value="1" />
            <output name="out_scatter_file" file="sample-scatter.pdf" ftype="pdf" compare="sim_size">
                <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[