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−<tool id="cnvkit_segment" name="CNVkit Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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−    <description>Infer copy number segments from the given coverage table</description>
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−    <macros>
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−        <import>macros.xml</import>
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−    </macros>
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−    <expand macro="xrefs"/>
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−    <expand macro="creators"/>
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−    <expand macro="requirements"/>
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−    <command detect_errors="exit_code"><![CDATA[  
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−        ln -s '$filename' ./tumor.cnr &&
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−        #if $additional_SNP_allelic_process.vcf
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−            ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
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−        #end if
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−        #import os
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−        cnvkit.py segment
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−            ./tumor.cnr
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−            --output sample.cns
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−            --processes \${GALAXY_SLOTS:-4}
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−            #if $advanced_settings.dataframe
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−                --dataframe '$advanced_settings.dataframe'
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−            #end if
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−            #if $advanced_settings.method == "cbs"
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−                #set $method_val = "cbs"
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−                --method '$method_val'
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−            #else
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−                --method '$advanced_settings.method'
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−            #end if
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−            #if str($advanced_settings.threshold)
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−                --threshold $advanced_settings.threshold
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−            #end if
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−            $advanced_settings.drop_low_coverage
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−            #if str($advanced_settings.drop_outliers)
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−                 --drop-outliers $advanced_settings.drop_outliers
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−            #end if
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−            $advanced_settings.smooth_cbs
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−            #if $additional_SNP_allelic_process.vcf
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−                 --vcf ./vcf_file.vcf
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−            #end if
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−            #if $additional_SNP_allelic_process.sample_id
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−                --sample-id '$additional_SNP_allelic_process.sample_id'
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−            #end if
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−            #if $additional_SNP_allelic_process.normal_id
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−                 --normal-id '$additional_SNP_allelic_process.normal_id'
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−            #end if
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−            #if str($additional_SNP_allelic_process.min_variant_depth)
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−                 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
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−            #end if
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−            #if str($additional_SNP_allelic_process.zygosity_freq)
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−                 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
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−            #end if
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−    ]]></command>
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−    <inputs>
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−        <param name="filename" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
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−        <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
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−            <expand macro="additionally_SNP_process" />
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−        </section>
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−        <section name="advanced_settings" title="Advanced settings" expanded="false">
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−            <expand macro="segment_optional" />
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−        </section>
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−    </inputs>
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−    <outputs>
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−        <data name="out_sample_segment" format="cns" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
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−    </outputs>
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−    <tests>
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−        <test expect_num_outputs="1">
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−            <param name="filename" ftype="cnr" value="tumor.cnr" />
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−            <section name="advanced_settings">
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−                <param name="method" value="hmm" />
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−                <param name="threshold" value="2" />
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−                <param name="drop_outliers" value="2" />
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−                <param name="drop_low_coverage" value="1" />
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−            </section>
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−            <output name="out_sample_segment">
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−                <assert_contents><has_text text="chromosome"/></assert_contents>
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−            </output>
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−        </test>
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−    </tests>
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−    <help><![CDATA[
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−         Infer copy number segments from the given coverage table. Segmentation runs independently on
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−         each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
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−         
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−         Segmented log2 ratios (.cns) output file contains those columns
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−          chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
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−    
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−-----
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−
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−**Bin-level log2 ratios (.cnr)**
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−
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−Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
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−
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−.. csv-table::
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−   :header-rows: 0
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−
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−    "chromosome","Genomic chromosome (e.g., chr1, chrX)"
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−    "start","Start position of the bin."
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−    "end","End position of the bin."
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−    "gene","Gene name(s) overlapping the bin (if applicable)."
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−    "log2","Normalized log2 ratio (sample coverage / reference coverage)."
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−    "depth","Average read depth in the bin."
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−    "weight","Reliability weight of the bin (higher = more reliable)."
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−
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−-----
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−
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−**Segmented log2 ratios (.cns)**
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−
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−Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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−
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−.. csv-table::
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−   :header-rows: 0
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−
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−    "chromosome","start, end: Genomic coordinates of the segment"
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−    "gene","Gene(s) overlapping the segment."
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−    "log2","Mean log2 ratio of the segment."
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−    "probes","Mean log2 ratio of the segment."
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−    "depth","Average read depth."
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−    "weight","Reliability weight."
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−    "p_value","Statistical confidence (lower = more significant)."
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−
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−    ]]></help>
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−    <expand macro="citations" />
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−</tool>