<commit_before><tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false">
    <requirements>
        <requirement type="package" version="2.2.1">requests</requirement>
        <requirement type="python-module">requests</requirement>
    </requirements>
    <description>CHASM score using CRAVAT webservice</description>
    <command interpreter="python">
        chasm_webservice.py --path $input
                            --analysis_type $analysis_type
                            --cancertype $tissue_type
                            --email $__user_email__
                            --gene_analysis_out $gene_analysis_out
                            --variant_analysis_out $variant_analysis_out
                            --amino_acid_level_analysis_out $amino_acid_level_analysis_out
                            --codon_level_analysis_out $codon_level_analysis_out
                            --error_file $error_file

    </command>
    <inputs>
        <param format="txt" name="input" type="data" label="Variants File" />
        <param name="analysis_type" type="select" label="Choose analysis type" help="
                                                                        Cancer driver analysis predicts whether\
                                                                        the submitted variants are cancer drivers.\
                                                                        Functional effect analysis predicts whether\
                                                                        the submitted variants will have any\
                                                                        functional effect on their translated proteins.\
                                                                        Annotation only provides\
                                                                        GeneCard and PubMed information on\
                                                                        the genes containing the submitted variants.">
            <option value="driver">Cancer driver analysis</option>
            <option value="functional">Functional effect analysis</option>
            <option value="geneannotationonly">Annotation only</option>
        </param>

        <param name="gene_annotation" type="select" label="Include Gene annotation">
            <option value="no">No</option>
            <option value="yes">Yes</option>
        </param>

        <param name="tissue_type" type="select" label="Tissue Type">
            <option value="Bladder">Bladder</option>
            <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
            <option value="Blood-Myeloid">Blood-Myeloid</option>
            <option value="Brain-Cerebellum">Brain-Cerebellum</option>
            <option value="Brain-Glioblastoma_Multiforme">Brain-Glioblastoma_Multiforme</option>
            <option value="Brain-Lower_Grade_Glioma">Brain-Lower_Grade_Glioma</option>
            <option value="Breast">Breast</option>
            <option value="Cervix">Cervix</option>
            <option value="Colon">Colon</option>
            <option value="Head_and_Neck">Head_and_Neck</option>
            <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
            <option value="Kidney-Clear_Cell">Kidney-Clear_Cell</option>
            <option value="Kidney-Papiallary_Cell">Kidney-Papiallary_Cell</option>
            <option value="Liver-Nonviral">Liver-Nonviral</option>
            <option value="Liver-Viral">Liver-Viral</option>
            <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
            <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option>
            <option value="Melanoma">Melanoma</option>
            <option value="Other">Other</option>
            <option value="Ovary">Ovary</option>
            <option value="Pancreas">Pancreas</option>
            <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
            <option value="Rectum">Rectum</option>
            <option value="Skin">Skin</option>
            <option value="Stomach">Stomach</option>
            <option value="Thyroid">Thyroid</option><commit_msg>Minor fix<commit_after><tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false">
    <requirements>
        <requirement type="package" version="2.2.1">requests</requirement>
        <requirement type="python-module">requests</requirement>
    </requirements>
    <description>CHASM score using CRAVAT webservice</description>
    <command interpreter="python">
        chasm_webservice.py --path $input
                            --analysis_type $analysis_type
                            --cancertype $tissue_type
                            --email $__user_email__
                            --gene_analysis_out $gene_analysis_out
                            --variant_analysis_out $variant_analysis_out
                            --amino_acid_level_analysis_out $amino_acid_level_analysis_out
                            --codon_level_analysis_out $codon_level_analysis_out
                            --error_file $error_file

    </command>
    <inputs>
        <param format="txt" name="input" type="data" label="Variants File" />
        <param name="analysis_type" type="select" label="Choose analysis type" help="
                                                                    Cancer driver analysis predicts whether\
                                                                    the submitted variants are cancer drivers.\
                                                                    Functional effect analysis predicts whether\
                                                                    the submitted variants will have any\
                                                                    functional effect on their translated proteins.\
                                                                    Annotation only provides\
                                                                    GeneCard and PubMed information on\
                                                                    the genes containing the submitted variants.">
            <option value="driver">Cancer driver analysis</option>
            <option value="functional">Functional effect analysis</option>
            <option value="geneannotationonly">Annotation only</option>
        </param>

        <param name="gene_annotation" type="select" label="Include Gene annotation">
            <option value="no">No</option>
            <option value="yes">Yes</option>
        </param>

        <param name="tissue_type" type="select" label="Tissue Type">
            <option value="Bladder">Bladder</option>
            <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
            <option value="Blood-Myeloid">Blood-Myeloid</option>
            <option value="Brain-Cerebellum">Brain-Cerebellum</option>
            <option value="Brain-Glioblastoma_Multiforme">Brain-Glioblastoma_Multiforme</option>
            <option value="Brain-Lower_Grade_Glioma">Brain-Lower_Grade_Glioma</option>
            <option value="Breast">Breast</option>
            <option value="Cervix">Cervix</option>
            <option value="Colon">Colon</option>
            <option value="Head_and_Neck">Head_and_Neck</option>
            <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
            <option value="Kidney-Clear_Cell">Kidney-Clear_Cell</option>
            <option value="Kidney-Papiallary_Cell">Kidney-Papiallary_Cell</option>
            <option value="Liver-Nonviral">Liver-Nonviral</option>
            <option value="Liver-Viral">Liver-Viral</option>
            <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
            <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option>
            <option value="Melanoma">Melanoma</option>
            <option value="Other" selected="true">Other</option>
            <option value="Ovary">Ovary</option>
            <option value="Pancreas">Pancreas</option>
            <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
            <option value="Rectum">Rectum</option>
            <option value="Skin">Skin</option>
            <option value="Stomach">Stomach</option>
            <option value="Thyroid">Thyroid</option>
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