comparison pharmcat.xml @ 1:8005ce1418ac draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"

0:28aa54c800c0

<tool id="pharmcat" name="pharmCAT" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
    <description>
        Pharmacogenomics Clinical Annotation Tool
    </description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.3.1</token>
        <token name="@VERSION_SUFFIX@">galaxy0</token>
    </macros>
    <requirements>
        <container type="docker">pgkb/pharmcat:1.3.1</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    ## NAMECALLER FUNCTION
        #if $function_select.function == 'name':
            ln -s '$function_select.input' ./input.vcf &&

                <option value="name">Only named allele matcher</option>
                <option value="pheno">Only phenotyper</option>
                <option value="report">Only reporter</option>
            </param>
            <when value="all">
                <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/>
                <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/>
                <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/>
                <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
            </when>
            <when value="name">
                <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
            </when>
            <when value="pheno">
                <conditional name="method">
                    <param name="pheno_function" type="select" label="Which function of PharmCAT should be run?">
                        <option value="vcf">Run directly from vcf samples</option>
                        <option value="named">Run from the output of the NamedAlleleMatcher</option>
                    </param>
                    <when value="vcf">
                        <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                    </when>
                    <when value="named">
                        <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/>
                    </when>
                </conditional>

    </outputs>
    <tests>
    <!-- ALL FUNCTION -->
        <test expect_num_outputs="3">
            <conditional name="function_select">
                <param name="input" ftype="vcf" value="test.vcf"/>
                <param name="outside_call" ftype="tabular" value="test.tsv"/>
                <param name="json" value="-j"/>
                <param name="phenojson" value="-pj"/>
            </conditional>
            <output name="all_out">
                <assert_contents>

        </test>
    <!-- NAMECALLER -->
        <test expect_num_outputs="2">
            <conditional name="function_select">
                <param name="function" value="name"/>
                <param name="input" ftype="vcf" value="test.vcf"/>
            </conditional>
            <output name="namer_html" file="test_2.html" lines_diff="2"/>
            <output name="namer_json" file="test_2.json" lines_diff="2"/>
        </test>
    <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER-->
        <test expect_num_outputs="1">
            <conditional name="function_select">
                <param name="function" value="pheno"/>

    <!-- PHENOTYPER FROM NAMECALLER AND NO OUTSIDE CALLER-->
        <test expect_num_outputs="1">
            <conditional name="function_select">
                <param name="function" value="pheno"/>
                <conditional name="method">
                    <param name="pheno_function" value="named"/>
                    <param name="input" value="test_2.json"/>
                </conditional>
            </conditional>
            <output name="pheno_json" file="test_4.json" lines_diff="1"/>
        </test>
    <!-- REPORTER -->
        <test expect_num_outputs="2">
            <conditional name="function_select">
                <param name="function" value="report"/>
                    <param name="input" value="test_3.json"/>
                    <param name="text" value="test text"/>
            </conditional>
            <output name="report_json">
                <assert_contents>
                    <has_text text="Implication for CYP2C19"/>
                    <has_text text="Lower dose-adjusted trough concentrations of tacrolimus and decreased chance of achieving target tacrolimus concentrations."/>

1:8005ce1418ac

<tool id="pharmcat" name="pharmCAT" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
    <description>
        Pharmacogenomics Clinical Annotation Tool
    </description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.7.0</token>
        <token name="@VERSION_SUFFIX@">galaxy0</token>
    </macros>
    <requirements>
        <container type="docker">pgkb/pharmcat:1.7.0</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    ## NAMECALLER FUNCTION
        #if $function_select.function == 'name':
            ln -s '$function_select.input' ./input.vcf &&

                <option value="name">Only named allele matcher</option>
                <option value="pheno">Only phenotyper</option>
                <option value="report">Only reporter</option>
            </param>
            <when value="all">
                <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
                    help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/>
                <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/>
                <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/>
                <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
            </when>
            <when value="name">
                <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
                    help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
            </when>
            <when value="pheno">
                <conditional name="method">
                    <param name="pheno_function" type="select" label="Which function of PharmCAT should be run?">
                        <option value="vcf">Run directly from vcf samples</option>
                        <option value="named">Run from the output of the NamedAlleleMatcher</option>
                    </param>
                    <when value="vcf">
                        <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
                            help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                    </when>
                    <when value="named">
                        <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/>
                    </when>
                </conditional>

    </outputs>
    <tests>
    <!-- ALL FUNCTION -->
        <test expect_num_outputs="3">
            <conditional name="function_select">
                <param name="input" value="test.vcf" ftype="vcf" />
                <param name="outside_call" value="test.tsv" ftype="tabular"/>
                <param name="json" value="-j"/>
                <param name="phenojson" value="-pj"/>
            </conditional>
            <output name="all_out">
                <assert_contents>

        </test>
    <!-- NAMECALLER -->
        <test expect_num_outputs="2">
            <conditional name="function_select">
                <param name="function" value="name"/>
                <param name="input" value="test.vcf" ftype="vcf"/>
            </conditional>
            <output name="namer_html" file="test_2.html" lines_diff="4" ftype="html" />
            <output name="namer_json" file="test_2.json" lines_diff="2" ftype="json" />
        </test>
    <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER-->
        <test expect_num_outputs="1">
            <conditional name="function_select">
                <param name="function" value="pheno"/>

    <!-- PHENOTYPER FROM NAMECALLER AND NO OUTSIDE CALLER-->
        <test expect_num_outputs="1">
            <conditional name="function_select">
                <param name="function" value="pheno"/>
                <conditional name="method">
                    <param name="pheno_function" value="named" />
                    <param name="input" value="test_2.json" ftype="json" />
                </conditional>
            </conditional>
            <output name="pheno_json" file="test_4.json" lines_diff="34"/>
        </test>
    <!-- REPORTER -->
        <test expect_num_outputs="2">
            <conditional name="function_select">
                <param name="input" value="test_3.json" ftype="json"/>
                <param name="function" value="report"/>
                <param name="text" value="test text"/>
            </conditional>
            <output name="report_json">
                <assert_contents>
                    <has_text text="Implication for CYP2C19"/>
                    <has_text text="Lower dose-adjusted trough concentrations of tacrolimus and decreased chance of achieving target tacrolimus concentrations."/>