annotate biosamples.xml @ 2:7e8a31232cdb draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit bf308a3ea09dc413670e41141d6849af7dd33798

<tool id="beacon2_biosamples" name="Beacon2 Biosamples" version="1.0.0" profile="21.05">
    <description>Query the biosamples collection in the beacon database for samples taken from individuals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        beacon2-search biosamples
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        #if str($advanced_settings.biosampleStatus)
            --biosampleStatus '$advanced_settings.biosampleStatus'
        #end if
        #if str($advanced_settings.collectionDate)
            --collectionDate '$advanced_settings.collectionDate'
        #end if
        #if str($advanced_settings.collectionMoment)
            --collectionMoment '$advanced_settings.collectionMoment'
        #end if
        #if str($advanced_settings.identification)
            --identification '$advanced_settings.identification'
        #end if
        #if str($advanced_settings.diagnosticMarkers)
            --diagnosticMarkers '$advanced_settings.diagnosticMarkers'
        #end if
        #if str($advanced_settings.histologicalDiagnosis)
            --histologicalDiagnosis '$advanced_settings.histologicalDiagnosis'
        #end if
        #if str($advanced_settings.obtentionProcedure)
            --obtentionProcedure '$advanced_settings.obtentionProcedure'
        #end if
        #if str($advanced_settings.pathologicalStage)
            --pathologicalStage '$advanced_settings.pathologicalStage'
        #end if
        #if str($advanced_settings.pathologicalTnmFinding)
            --pathologicalTnmFinding '$advanced_settings.pathologicalTnmFinding'
        #end if
        #if str($advanced_settings.featureType)
            --featureType '$advanced_settings.featureType'
        #end if
        #if str($advanced_settings.severity)
            --severity '$advanced_settings.severity'
        #end if
        #if str($advanced_settings.sampleOriginDetail)
            --sampleOriginDetail '$advanced_settings.sampleOriginDetail'
        #end if
        #if str($advanced_settings.sampleOriginType)
            --sampleOriginType '$advanced_settings.sampleOriginType'
        #end if
        #if str($advanced_settings.sampleProcessing)
            --sampleProcessing '$advanced_settings.sampleProcessing'
        #end if
        #if str($advanced_settings.sampleStorage)
            --sampleStorage '$advanced_settings.sampleStorage'
        #end if
        #if str($advanced_settings.tumorGrade)
            --tumorGrade '$advanced_settings.tumorGrade'
        #end if
        #if str($advanced_settings.tumorProgression)
            --tumorProgression '$advanced_settings.tumorProgression'
        #end if
        > biosamples_query_findings.json
        ]]>
    </command>
    <expand macro="configfile"/>
    <inputs>
        <expand macro="Connection_to_MongoDB"/>
        <expand macro="Database_Configuration"/>
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--biosampleStatus" optional="true" type="text" label="BIOSAMPLE STATUS" value="" help="Ontology value for the classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654)" />
            <param argument="--collectionDate" optional="true" type="text" label="COLLECTION DATE" value="" help="Date of biosample collection in ISO8601 format" />
            <param argument="--collectionMoment" optional="true" type="text" label="COLLECTION MOMENT" value="" help="Individual's or cell culture age at the time of sample collection in the ISO8601 duration format P[n]Y[n]M[n]DT[n]H[n]M[n]S, e.g. P32Y6M1D, P7D" />
            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Biosample identifier (external accession or internal ID)" />
            <param argument="--diagnosticMarkers" optional="true" type="text" label="DIAGNOSTIC MARKERS" value="" help="Clinically relevant bio markers, e.g. T2b Stage Finding" />
            <param argument="--histologicalDiagnosis" optional="true" type="text" label="HISTOLOGICAL DIAGNOSIS" value="" help="Disease diagnosis that was inferred from the histological examination, e.g. Serous Cystadenocarcinoma" />
            <param argument="--obtentionProcedure" optional="true" type="text" label="OBTENTION PROCEDURE" value="" help="Ontology value describing the procedure for sample obtention, e.g. biopsy" />
            <param argument="--pathologicalStage" optional="true" type="text" label="PATHOLOGICAL STAGE" value="" help="Pathological stage, if applicable, e.g. Stage IIIA" />
            <param argument="--pathologicalTnmFinding" optional="true" type="text" label="PATHOLOGICAL TNM FINDING" value="" help="T2b Stage Finding" />
            <param argument="--featureType" optional="true" type="text" label="FEATURE TYPE" value="" help="Definition of an ontology term which describes the phenotype, e.g. Infantile spasms" />
            <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="Ontology class that describes the severity of the condition, e.g. Moderate" />
            <param argument="--sampleOriginDetail" optional="true" type="text" label="SAMPLE ORIGIN DETAIL" value="" help="Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType', e.g. wall of urinary bladder" />
            <param argument="--sampleOriginType" optional="true" type="text" label="SAMPLE ORIGIN TYPE" value="" help="Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity, e.g abnormal sample" />
            <param argument="--sampleProcessing" optional="true" type="text" label="SAMPLE PROCESSING" value="" help="Status of how the specimen was processed, e.g. mechanical dissociation" />
            <param argument="--sampleStorage" optional="true" type="text" label="SAMPLE STORAGE" value="" help="Status of how the specimen was stored" />
            <param argument="--tumorGrade" optional="true" type="text" label="TUMOR GRADE" value="" help="Term representing the tumor grade, e.g. Grade 3a" />
            <param argument="--tumorProgression" optional="true" type="text" label="TUMOR PROGRESSION" value="" help="Tumor progression category indicating primary, metastatic or recurrent progression, e.g. Primary Malignant Neoplasm" />
        </section>
    </inputs>
    <outputs>
        <data name="out_biosamples_query" format="json" label="${tool.name} on ${on_string}: Biosamples Query" from_work_dir="biosamples_query_findings.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="database" value="beacon" />
            <param name="collection" value="test" />
            <param name="db_host" value="20.108.51.167" />
            <param name="tumorGrade" value="Grade 2 Lesion" />
            <param name="biosampleStatus" value="abnormal sample" />
            <param name="collectionDate" value="2021-04-23" />
            <param name="sampleOriginDetail" value="wall of urinary bladde" />
            <param name="tumorProgression" value="Primary Malignant Neoplasm" />
            <output name="out_biosamples_query">
                <assert_contents>
                    <has_text_matching expression="_id"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Beacon2 Biosamples queries the biosamples collection in the Beacon database for samples taken from individuals. This tool allows detailed queries using advanced settings such as biosample status, collection date, diagnostic markers, and more.
    ]]></help>
    <expand macro="citations" />
</tool>