annotate batch.xml @ 2:ec07e22c41f8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit bced16a45d19b243a244a093c3b3504b2640d5e0

<tool id="cnvkit_batch" name="CNVkit Batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Run the CNVkit pipeline on one or more BAM files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[   
        ln -s '$CNV_reference.input_sample_file' ./tumor.bam &&
        ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai &&
        #if str($CNV_reference.CNV_reference_availabel) == "yes":
            ln -s '$CNV_reference.reference' ./reference.cnn &&
        #end if 
        #if str($CNV_reference.CNV_reference_availabel) == "no":
            ln -s '$CNV_reference.normal' ./normal.bam &&
            ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai &&
            #if $CNV_reference.advanced_settings.antitargets
                ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed &&
            #end if
            #if $CNV_reference.advanced_settings.annotate
                ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed &&
            #end if
            #if $CNV_reference.advanced_settings.access
                ln -s '$CNV_reference.advanced_settings.access' ./access.bed &&
            #end if
            ln -s '$CNV_reference.targets' ./capture.bed &&
            #if str($CNV_reference.reference_source.ref_selector) == 'history':
                ln -s '$CNV_reference.reference_source.fasta' ./genome.fa &&
                samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
            #else
                ln -s '$CNV_reference.reference_source.fasta.fields.path' ./genome.fa &&
                ln -s '${CNV_reference.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
            #end if
        #end if
        #import os
        cnvkit.py batch
            ./tumor.bam
            #if str($CNV_reference.CNV_reference_availabel) == "no":
                --normal ./normal.bam
                --targets ./capture.bed
                --fasta ./genome.fa
                #if $CNV_reference.advanced_settings.antitargets
                    --antitargets ./antitargets.bed
                #end if
                #if $CNV_reference.advanced_settings.annotate
                    --annotate ./annotate.bed
                #end if
                #if $CNV_reference.advanced_settings.access
                    --access ./access.bed
                #end if
            #end if
            #if str($CNV_reference.CNV_reference_availabel) == "yes":
                --reference ./reference.cnn
            #end if
            $output_section.scatter
            $output_section.diagram
            --processes \${GALAXY_SLOTS:-4}
            #if $CNV_reference.advanced_settings.method == "hybrid"
                #set $method_val = "hybrid"
                --method '$method_val'
            #else
                --method '$CNV_reference.advanced_settings.method'
            #end if
            
            #if $CNV_reference.advanced_settings.segment_method == "cbs"
                #set $segment_method_val = "cbs"
                --segment-method '$segment_method_val'
            #else
                --segment-method '$CNV_reference.advanced_settings.segment_method'
            #end if
            $CNV_reference.advanced_settings.male_reference
            $CNV_reference.advanced_settings.countreads
            $CNV_reference.advanced_settings.drop_low_coverage
            
            #if str($CNV_reference.CNV_reference_availabel) == "no":
                $CNV_reference.advanced_settings.short_names
                #if str($CNV_reference.advanced_settings.target_avg_size)
                    --target-avg-size $CNV_reference.advanced_settings.target_avg_size
                #end if 
                #if str($CNV_reference.advanced_settings.antitarget_avg_size)
                    --antitarget-avg-size $CNV_reference.advanced_settings.antitarget_avg_size
                #end if
                #if str($CNV_reference.advanced_settings.antitarget_min_size)
                    --antitarget-min-size $CNV_reference.advanced_settings.antitarget_min_size
                #end if 
                $CNV_reference.advanced_settings.cluster
            #end if            
    ]]></command>
    <inputs>
        <conditional name="CNV_reference">
            <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file (.cnn)?" help="">
                <option value="no" selected="True">Build a new copy number reference file</option>
                <option value="yes">Reuse a copy number reference file</option>
            </param>
            <when value="no">
                <expand macro="create_CNV_reference_file" />
                <expand macro="reference_interface" />
                <section name="advanced_settings" title="Advanced settings" expanded="false">
                    <expand macro="advanced_no_reference" />
                    <expand macro="shared" />
                </section>
            </when>
            <when value="yes">
                <expand macro="reuse_an_existing_cnv_reference_file" />
                <section name="advanced_settings" title="Advanced settings" expanded="false">
                    <expand macro="shared" />
                </section>
            </when>
        </conditional>
        <expand macro="output_section" />
    </inputs>
    <outputs>
        <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
        <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
        <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
        <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
        <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
        <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
        <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
        </data>
        <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
        </data>
        <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
        </data>
        <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
        </data>
        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
        </data>
        <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
        </data>
        <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
            <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
        </data>
        <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Sample Diagram" from_work_dir="tumor-diagram.pdf">
            <filter>output_section['diagram']</filter>
        </data>
        <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Sample Scatter pdf plot " from_work_dir="tumor-scatter.png">
            <filter>output_section['scatter']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="13">
            <conditional name="reference_source">
                <param name="ref_selector" value="history"/>
                <param name="fasta" ftype="fasta" value="genome.fasta" />
            </conditional>
            <param name="CNV_reference_availabel" value="no" />
            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
            <param name="normal" ftype="bam" value="normal.bam" />
            <param name="targets" ftype="bed" value="capture.bed" />
            <param name="scatter" value="1"/>
            <param name="diagram" value="1"/>
            <output name="out_sample_bintest" file="tumor.bintest.cns" />
            <output name="out_sample_antitargetcoverage">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_call">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_cnr">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_targetcoverage_cnn">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_cns">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_capture_antitarget" file="capture.antitarget.bed" />
            <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
            <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
            <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
                <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
            </output>
            <output name="out_capture_target">
                <assert_contents><has_text_matching expression="chrM"/></assert_contents>
            </output>
            <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
                <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
            </output>                        
            <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
                <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
            </output>
        </test>
        <test expect_num_outputs="13">
            <conditional name="reference_source">
                <param name="ref_selector" value="cached"/>
                <param name="fasta" value="test_buildid"/>
            </conditional>
            <param name="CNV_reference_availabel" value="no" />
            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
            <param name="normal" ftype="bam" value="normal.bam" />
            <param name="targets" ftype="bed" value="capture.bed" />
            <param name="scatter" value="1"/>
            <param name="diagram" value="1"/>
            <output name="out_sample_bintest" file="tumor.bintest.cns" />
            <output name="out_sample_antitargetcoverage">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_call">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_cnr">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_targetcoverage_cnn">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_cns">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_capture_antitarget" file="capture.antitarget.bed" />
            <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
            <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
            <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
                <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
            </output>
            <output name="out_capture_target">
                <assert_contents><has_text_matching expression="chrM"/></assert_contents>
            </output>
            <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
                <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
            </output>                        
            <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
                <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
            </output>
        </test>
        <test expect_num_outputs="10">
            <param name="CNV_reference_availabel" value="yes" />
            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
            <param name="reference" ftype="tabular" value="reference.cnn" />
            <param name="scatter" value="1"/>
            <param name="diagram" value="1"/>
            <output name="out_sample_bintest" file="tumor.bintest.cns" />
            <output name="out_sample_antitargetcoverage">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_call">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_cnr">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_targetcoverage_cnn">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_sample_cns">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
            <output name="out_reference_target_bed" file="reference.target-tmp.bed" />
            <output name="out_reference_antitarget_bed" file="reference.antitarget-tmp.bed" />
            <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
                <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
            </output>
            <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
                <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
          CNVkit pipeline for  copy-number changes and allelic imbalances detection
          cnn, cnr and cns are tabuler files extintions:
          
          The reference .cnn file has the columns:
          chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
          of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
          depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
          
          Target and antitarget bin-level coverages (.cnn)
          chromosome, Start, end, gene, log2 and depth
          
          Bin-level log2 ratios (.cnr)
          chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight)
          
          Segmented log2 ratios (.cns)
          chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
          
          
    ]]></help>
    <expand macro="citations" />
</tool>