annotate breaks.xml @ 0:ef9a50eb20ce draft

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

<tool id="cnvkit_breaks" name="CNVkit Breaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>List the targeted genes with segmentaion breakpoint</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators_and_zahra"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_filename_file' ./sample.cnr &&
        ln -s '$input_segment_file' ./sample.cns &&
        cnvkit.py breaks
            ./sample.cnr
            ./sample.cns 
            --output gene-breaks.txt
            #if $min_probes
                --min-probes $min_probes
            #end if                    
    ]]></command>
    <inputs>
        <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" />
        <param name="input_segment_file" type="data"  format="tabular" label="CN segmentation calls cnn file" help="The output of the CNVkit segment" />
        <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" />     
    </inputs>
    <outputs>
        <data name="gene_breaks" format="text" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
            <param name="input_segment_file" ftype="tabular" value="sample.cns" />
            <param name="min_probes" value="1" />
            <output name="gene_breaks">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output> 
        </test>
    </tests>
    <help><![CDATA[
        
       Identify genes in which: 
       (I) an unbalanced fusion or other structural rearrangement breakpoint occured
       (II) CNV calling is simply difficult due to an inconsistent copy number signal
       
       The breaks output is a text table of tab-separated values, which is amenable to further processing by 
       scripts and standard Unix tools such as grep, sort, cut and awk. 
    ]]></help>
    <expand macro="citations" />
</tool>