view chasm_webservice/chasm_webservice.xml @ 0:99d838cef41a draft default tip

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<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="package" version="0.9.3">xlrd</requirement>
        <requirement type="python-module">requests</requirement>
        <requirement type="python-module">xlrd</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>
            <option value="Uterus">Uterus</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="gene_analysis_out" label="${tool.name} on ${on_string}: genes" />
        <data format="tabular" name="variant_analysis_out" label="${tool.name} on ${on_string}: variant" />
        <data format="tabular" name="amino_acid_level_analysis_out" label="${tool.name} on ${on_string}: aminoacid" />
        <data format="tabular" name="error_file" label="${tool.name} on ${on_string}: error" />
        <data format="tabular" name="codon_level_analysis_out" label="${tool.name} on ${on_string}: Codon level" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="chasm_input.txt"/>
            <param name="gene_annotation" value="no"/>
            <param name="analysis_type" value="driver"/>
            <param name="tissue_type" value="Other"/>
            <output name="gene_analysis_out" file="chasm_output_genes.tabular" lines_diff="4" ftype="tabular"/>
            <output name="variant_analysis_out" file="chasm_output_variants.tabular" lines_diff="4"/>
            <output name="amino_acid_level_analysis_out" file="chasm_output_aminoacids.tabular"/>
            <output name="error_file" file="chasm_output_errors.tabular" lines_diff="4"/>
            <output name="codon_level_analysis_out" file="chasm_output_codons.tabular" lines_diff="4"/>
        </test>
    </tests>

    <help>
        **What it does**


        CRAVAT: Cancer-Related Analysis of VAriants Toolkit is a web server with simple interface where cancer-related analysis of variants are performed. To cite CRAVAT, please use this article.

        CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST

        **Input**

        -Comment lines start with ">", "#", or "!".


        -Data fields are separated by a tab or a space.


        -The following two formats can be used for input data, but all the data rows should be in the same format:

        .. class:: infomark

        Genomic-coordinate format (separated by a tab or a space):


        # UID / Chr. / Position / Strand / Ref. base / Alt. base / Sample ID (optional)
        TR1	chr17	7577506	-	G	T	TCGA-02-0231


        TR2	chr10	123279680	-	G	A	TCGA-02-3512


        TR3	chr13	49033967	+	C	A	TCGA-02-3532


        TR4	chr7	116417505	+	G	T	TCGA-02-1523


        TR5	chr7	140453136	-	T	A	TCGA-02-0023


        TR6	chr17	37880998	+	G	T	TCGA-02-0252


        Ins1 chr17	37880998	+	G	GT	TCGA-02-0252


        Del1 chr17	37880998	+	GA	G	TCGA-02-0252


        CSub1 chr2	39871235	+	ATGCT	GA	TCGA-02-0252



        Position is a 1-based open coordinate. For insertions and deletions, use the base before the insertion or the
        first base of the deletion as the reference base. If you do not have strand information from your sequencing results,
        it is likely that they are all reported on the + strand.
        Make sure that your reported reference base matches the base in the reported position in the
        hg19 reference sequence (or hg18 if you checked hg18 checkbox).

        .. class:: infomark

        Amino-acid residue substitution format (separated by a tab or a space):


        # UID / Transcript / AA change / Sample ID (optional)


        TR1	NM_001126116.1	D127Y	TCGA-02-0231


        TR2	NM_001144919.1	R162Q	TCGA-02-3512


        TR3	NM_000321.2	Q702K	TCGA-02-3532


        TR4	NM_000245.2	A1108S	TCGA-02-1523


        TR5	NM_004333.4	V600E	TCGA-02-0023


        TR6	NM_001005862.1	G746V	TCGA-02-0252


        trascript identifier can be from either NCBI Refseq, CCDS, or Ensembl.
        Refseq and CCDS accessions can be specified without version numbers.
        The format of "AA change" column is (reference AA)(AA position)(alternate AA), without "(" and ")".
        Reference and alternate AAs should be from the 20 essential amino acids and each of them should be one amino acid-long.


        **Analysis**


        .. class:: infomark


        Analysis Type:


        -*Cancer driver analysis*: This analysis predicts whether the submitted variants are cancer drivers or not.


        -*Functional effect analysis*: This analysis predicts whether the submitted variants will have any functional effect on their translated proteins or not.


        -*Gene annotation only*: This analysis provides GeneCard and PubMed information on the genes containing the submitted variants.


        Currently, the following tissue types can be chosen at CRAVAT.


        Name	Full name	Source	Date


        Bladder	Bladder Urothelial Carcinoma	BLCA (TCGA)	Jun 2013


        Blood-Lymphocyte	Chronic Lymphocytic Leukemia	CLL (ICGC)	Mar 2013


        Blood-Myeloid	Acute Myeloid Leukemia	LAML (TCGA)	Jun 2013


        Brain-Cerebellum	Medulloblastoma	MB (mixed source)	Dec 2010


        Brain-Glioblastoma-Multiforme	Glioblastoma Multiforme	GBM (TCGA)	Jun 2013


        Brain-Lower-Grade-Glioma	Brain Lower Grade Glioma	LGG (TCGA)	Jun 2013


        Breast	Breast Invasive Carcinoma	BRCA (TCGA)	Jun 12012


        Cervix	Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma	CESC (TCGA)	Jun 2013


        Colon	Colon Adenocarcinoma	COAD (TCGA)	Jun 2013


        Head and Neck	Head and Neck Squamous Cell Carcinoma	HNSC (TCGA)	Jun 2013


        Kidney-Chromophobe	Kidney Chromophobe	KICH (TCGA)	Jun 2013


        Kidney-Clear-Cell	Kidney Renal Clear Cell Carcinoma	KIRC (TCGA)	Jun 2013


        Kidney-Papillary-Cell	Kidney Renal Papillary Cell Carcinoma	KIRP (TCGA)	Jun 2013


        Liver-Nonviral	Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity)	HCCA (ICGC)	Mar 2013


        Liver-Viral	Hepatocellular Carcinoma (Viral)	HCCV (ICGC)	Mar 2013


        Lung-Adenocarcinoma	Lung Adenocarcinoma	LUAD (TCGA)	Jun 2013


        Lung-Squamous Cell	Lung Squamous Cell Carcinoma	LUSC (TCGA)	Jun 2013


        Melanoma	Melanoma	ML (Yardena Samuels lab)	Dec 2011


        Other	General purpose	OV (TCGA)	Jun 2013


        Ovary	Ovarian Serous Cystadenocarcinoma	OV (TCGA)	Jun 2013


        Pancreas	Pancreatic Cancer	PNCC (ICGC))	Mar 2013


        Prostate-Adenocarcinoma	Prostate Adenocarcinoma	PRAD (TCGA)	Jun 2013


        Rectum	Rectum Adenocarcinoma	READ (TCGA)	Jun 2013


        Skin	Skin Cutaneous Melanoma	SKCM (TCGA)	Jun 2013


        Stomach	Stomach Adenocarcinoma	STAD (TCGA)	Jun 2013


        Thyroid	Thyroid Carcinoma	THCA (TCGA)	Jun 2013


        Uterus	Uterine Corpus Endometriod Carcinoma	UCEC (TCGA)	Jun 2013

        **Citation**

        If  you use this tool please cite:

        Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013). CRAVAT: Cancer-Related Analysis of VAriants Toolkit Bioinformatics, 29(5):647-648.

    </help>
</tool>