comparison seq_to_db.xml @ 3:39101f8f26dd draft default tip

planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit e8c8f102cab10531ed588be4ecb8a0d01e797f09

2:dad2c4c3450a

        #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
        #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
        python '$__tool_directory__/save_to_db.py'
            --input '$genbank_file_paths'
            --use_json_paramers '$json_use.use_json_paramers'
            #if not $json_use.use_json_paramers:
                --sequence_column '$json_use.sequence_column'
                --annotation_column '$json_use.annotation_column'
                --db_uri '$json_use.db_uri' 
                --table '$json_use.table' 
                --fragment_column '$json_use.fragment_column'

            --json_output '$json_output'
    ]]></command>
        <inputs>
        <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
        <conditional name="json_use">
            <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
            <when value="false">
                <param name="execution_enable" type="boolean" checked='true' label="Send Requenst to DB" help="enable or desable the interaction with the DB (can be usefull in workflows)" />
                <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'table'-" />
                <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" help="It can be extracted from JSON file -key:'sequence_column'-" />
                <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" help="It can be extracted from JSON file -key:'annotation_column'-" />

    </outputs>
    <tests>
        <!--test tool blocking from galaxy. It is commented because it should faild as it is a test to validate that the tool can be blocked from json file -->
        <test expect_num_outputs="2"> 
            <param name="genbank_files">
                <conditional type="list">
                    <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
                    <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
                    <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
                    <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
                    <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
                </conditional>
            </param>
            <conditional name="json_use">
                <param name='use_json_paramers' value='false' />
                <param name="table" value="sample" />
                <param name="sequence_column" value="sequence" />
                <param name="annotation_column" value="annotation" />
                <param name="fragment_column" value="fragment" />
                <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
                <param name="execution_enable" value="false" />
            </conditional>
            <param name="use_json_paramers" value='true'/>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="0" />
                </assert_contents>
            </output>

            <conditional name="json_use">
                <param name="use_json_paramers" value='true'/>
                <param name="json_conf" value="test-JSON_arg_block.json" />
            </conditional>
            <param name="json_generating" value='false'/>
            <param name="json_conf" value="test-JSON_arg_block.json" />
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="0" />
                </assert_contents>
            </output>

                <param name="annotation_column" value="annotation" />
                <param name="fragment_column" value="fragment" />
                <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
                <param name="execution_enable" value="true" />
            </conditional>
            <param name="use_json_paramers" value='true'/>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="5" />
                     <has_line_matching expression="p7_L7Ae-Weiss" />
                     <has_line_matching expression="p6_Nt-IgKLsequence" />

            </param>
            <conditional name="json_use">
                <param name="use_json_paramers" value='true'/>
                <param name="json_conf" value="test-JSON_arg.json" />
            </conditional>
            <param name="json_generating" value='false'/>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="5" />
                     <has_line_matching expression="p7_L7Ae-Weiss" />
                     <has_line_matching expression="p6_Nt-IgKLsequence" />

3:39101f8f26dd

        #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
        #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
        python '$__tool_directory__/save_to_db.py'
            --input '$genbank_file_paths'
            --use_json_paramers '$json_use.use_json_paramers'
            #if $json_use.use_json_paramers=='false':
                --sequence_column '$json_use.sequence_column'
                --annotation_column '$json_use.annotation_column'
                --db_uri '$json_use.db_uri' 
                --table '$json_use.table' 
                --fragment_column '$json_use.fragment_column'

            --json_output '$json_output'
    ]]></command>
        <inputs>
        <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
        <conditional name="json_use">
            <param name="use_json_paramers" type="select" checked='false' label="Use parameters from JSON" help="extract parameters from json file">
                <option value="true">Get Parameters From JSON</option>
                <option value="false" selected="true">Set Parameters Manually</option>
            </param>
            <when value="false">
                <param name="execution_enable" type="boolean" checked='true' label="Send Requenst to DB" help="enable or desable the interaction with the DB (can be usefull in workflows)" />
                <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'table'-" />
                <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" help="It can be extracted from JSON file -key:'sequence_column'-" />
                <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" help="It can be extracted from JSON file -key:'annotation_column'-" />

    </outputs>
    <tests>
        <!--test tool blocking from galaxy. It is commented because it should faild as it is a test to validate that the tool can be blocked from json file -->
        <test expect_num_outputs="2"> 
            <param name="genbank_files">
                <collection type="list">
                    <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
                    <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
                    <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
                    <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
                    <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
                </collection>
            </param>
            <conditional name="json_use">
                <param name='use_json_paramers' value='false' />
                <param name="table" value="sample" />
                <param name="sequence_column" value="sequence" />
                <param name="annotation_column" value="annotation" />
                <param name="fragment_column" value="fragment" />
                <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
                <param name="execution_enable" value="false" />
            </conditional>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="0" />
                </assert_contents>
            </output>

            <conditional name="json_use">
                <param name="use_json_paramers" value='true'/>
                <param name="json_conf" value="test-JSON_arg_block.json" />
            </conditional>
            <param name="json_generating" value='false'/>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="0" />
                </assert_contents>
            </output>

                <param name="annotation_column" value="annotation" />
                <param name="fragment_column" value="fragment" />
                <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
                <param name="execution_enable" value="true" />
            </conditional>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="5" />
                     <has_line_matching expression="p7_L7Ae-Weiss" />
                     <has_line_matching expression="p6_Nt-IgKLsequence" />

            </param>
            <conditional name="json_use">
                <param name="use_json_paramers" value='true'/>
                <param name="json_conf" value="test-JSON_arg.json" />
            </conditional>
            <output name="output" file="test_raport.txt" ftype="txt" >
                <assert_contents>
                     <has_n_lines n="5" />
                     <has_line_matching expression="p7_L7Ae-Weiss" />
                     <has_line_matching expression="p6_Nt-IgKLsequence" />