comparison reference.xml @ 2:0c3db8ec44b0 draft

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

1:83470ecad188

    <description>Compile a copy-number reference from the given files or directory containing normal samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        #import re
        #if str($CNV_reference.CNV_reference_availabel) == "yes"
            #set $names = []
            #set $x=1
            #for $x, $input in enumerate($CNV_reference.input_cnn_file):
                #set $name_base = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
                #set $name = $name_base + '_' + str(x)
                #silent $names.append( $name )
                ln -s '$input' ${name}.cnn  &&
            #end for
        #end if
        #if str($CNV_reference.CNV_reference_availabel) == "no"

                <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
                    <expand macro="disable_specific_automatic_bias_corrections" />
                </section>
            </when>
            <when value="yes">
                <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="cnn file" help="Normal-sample target or antitarget cnn files, or the directory that contains them" />
                <section name="advanced_settings" title="Advanced settings" expanded="false">
                    <expand macro="reference_interface" />
                    <expand macro="reference_optional" />
                    <expand macro="sample_sex_condition" />
                </section>

            <conditional name="reference_source">
                <param name="ref_selector" value="cached"/>
                <param name="fasta" value="test_buildid"/>
            </conditional>
            <param name="CNV_reference_availabel" value="yes" />
            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,sample.targetcoverage.cnn" />
            <param name="no_gc" value="1" />
            <output name="out_referene_tas">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
        </test>

            <conditional name="reference_source">
                <param name="ref_selector" value="cached"/>
                <param name="fasta" value="test_buildid"/>
            </conditional>
            <conditional name="Sample_sex">
                <param name="sex" value="yes" />
            </conditional>
            <param name="CNV_reference_availabel" value="no" />
            <param name="targets" ftype="bed" value="capture.target.bed" />
            <param name="no_gc" value="1" />
            <output name="out_referene_tas">

2:0c3db8ec44b0

    <description>Compile a copy-number reference from the given files or directory containing normal samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        #import re
        #if str($CNV_reference.CNV_reference_availabel) == "yes"
            #set $names = []
            #set $x=1
            #for $x, $input in enumerate($CNV_reference.input_cnn_file):
                #set $name_base = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
                #set $name = $name_base
                #silent $names.append( $name )
                ln -s '$input' ${name}.cnn  &&
            #end for
        #end if
        #if str($CNV_reference.CNV_reference_availabel) == "no"

                <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
                    <expand macro="disable_specific_automatic_bias_corrections" />
                </section>
            </when>
            <when value="yes">
                <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="Sample Target/antitarget Coverage cnn file" help="" />
                <section name="advanced_settings" title="Advanced settings" expanded="false">
                    <expand macro="reference_interface" />
                    <expand macro="reference_optional" />
                    <expand macro="sample_sex_condition" />
                </section>

            <conditional name="reference_source">
                <param name="ref_selector" value="cached"/>
                <param name="fasta" value="test_buildid"/>
            </conditional>
            <param name="CNV_reference_availabel" value="yes" />
            <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
            <param name="no_gc" value="1" />
            <output name="out_referene_tas">
                <assert_contents><has_text text="chromosome"/></assert_contents>
            </output>
        </test>

            <conditional name="reference_source">
                <param name="ref_selector" value="cached"/>
                <param name="fasta" value="test_buildid"/>
            </conditional>
            <conditional name="Sample_sex">
                <param name="sex" value="no" />
            </conditional>
            <param name="CNV_reference_availabel" value="no" />
            <param name="targets" ftype="bed" value="capture.target.bed" />
            <param name="no_gc" value="1" />
            <output name="out_referene_tas">