annotate logex.xml @ 5:0cae005d8c4c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b

<tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy5" profile="24.2" license="MIT">
    <description>Performs binary operations on the generated Ktab files from FASTK suite</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p logex_ktabs &&
        mkdir -p input_files &&
        #if $input_type.input_type_selector != 'collection'
            cp '$input_ktab1' input_files/input1.ktab &&
            ln -s '$input_ktab1_tar' input1.tar &&
            tar -xf input1.tar && 
            mv ktabfiles ktabfiles_in1 &&
            mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1" &&
            cp '$input_ktab2' input_files/input2.ktab &&
            ln -s '$input_ktab2_tar' input2.tar &&
            tar -xf input2.tar &&
            mv ktabfiles ktabfiles_in2 &&
            mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1" &&
            mv ktabfiles_in1/.input1.ktab.1 input_files/ &&
            mv ktabfiles_in2/.input2.ktab.1 input_files/ &&
            #if $input_type.operation_selector == 'and'
                Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab &&
            #elif $input_type.operation_selector == 'or'
                Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab &&
            #elif $input_type.operation_selector == 'minus'
                Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab &&
            #elif $input_type.operation_selector == 'xor'
                Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab && 
            #elif $input_type.operation_selector == 'unionsum'
                Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab &&
            #end if
        #else
            #for $i, $j in enumerate($input_type.input_ktab_collection):
                cp "$j" input_files/${i+1}.ktab &&
            #end for
            #for $p, $q in enumerate($input_type.input_ktab_collection_tar):
                ln -s "$q" input_files/input_ktab_${p+1}.tar &&
                tar -tf input_files/input_ktab_${p+1}.tar | grep '/\.[^/]*$' | tar --strip-components=1 -xf input_files/input_ktab_${p+1}.tar -C input_files/ -T - &&
                for file_name in input_files/.output.ktab.*; do
                    if [ -f "\$file_name" ]; then
                        new_name=\$(echo "\$file_name" | sed "s/\.output\.ktab\./\.$((p+1))\.ktab\./");
                        mv "\$file_name" "\$new_name";
                    fi
                done &&
                rm input_files/input_ktab_${p+1}.tar &&
            #end for
            COUNT=\$(ls -1 input_files/*.ktab 2>/dev/null | wc -l) &&
            if [ "\$COUNT" -ge 2 ]; then
                #if $input_type.operation_sel.operation_selector_collection == 'unionsum':
                    EXPRESSION="out=\$(seq -s '&+' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&                   
                #elif $input_type.operation_sel.operation_selector_collection == 'and':
                    EXPRESSION="out=\$(seq -s '&.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
                #elif $input_type.operation_sel.operation_selector_collection == 'minus':
                    EXPRESSION="out=\$(seq -s '-' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
                #elif $input_type.operation_sel.operation_selector_collection == 'or':
                    EXPRESSION="out=\$(seq -s '|.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
                #elif $input_type.operation_sel.operation_selector_collection == 'xor':
                    EXPRESSION="out=\$(seq -s '^' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
                #elif $input_type.operation_sel.operation_selector_collection == 'custom':
                    EXPRESSION="out=$input_type.operation_sel.custom_expression" &&
                #end if
                Logex -T\${GALAXY_SLOTS:-8} -h "\$EXPRESSION" input_files/*.ktab;   
            else
                echo "ERROR: Logex needs atleast 2 Ktab files" >&2 && exit 1;
            fi &&
        #end if
        cp *.ktab logex_ktabs/ &&
        cp .*.ktab* logex_ktabs/ &&
        tar -cf logex_ktab.tar input_files/ logex_ktabs/
    ]]></command>
    <inputs>
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="Single Ktab file or Ktab Collection">
                <option value="single">Single Ktab file</option>
                <option value="collection">Ktab files Collection</option>
            </param>
            <when value="single">
                <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/>
                <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
                <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
                <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
                <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
                    <option value="and">AND</option>
                    <option value="or">OR</option>
                    <option value="minus">Minus</option>
                    <option value="unionsum">Unionsum</option>
                    <option value="xor">XOR</option>
                </param>
            </when>
            <when value="collection">
                <param name="input_ktab_collection" type="data_collection" collection_type="list" format="fastk_ktab" label="Input FastK ktab Collection"/>
                <param name="input_ktab_collection_tar" type="data_collection" collection_type="list" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
                <conditional name="operation_sel">
                    <param name="operation_selector_collection" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
                        <option value="and">AND</option>
                        <option value="or">OR</option>
                        <option value="minus">Minus</option>
                        <option value="unionsum">Unionsum</option>
                        <option value="xor">XOR</option>
                        <option value="custom">Custom Logical Expression</option>
                    </param>
                    <when value="and"/>
                    <when value="or"/>
                    <when value="minus"/>
                    <when value="unionsum"/>
                    <when value="xor"/>
                    <when value="custom">
                        <param name="custom_expression" type="text" label="Custom Logical Expression" value="out=" help="Enter a custom logical expression based on number of your input ktab files. For Eg: For 3 Ktab files the expression can be out=(A^B)-C">
                            <sanitizer invalid_char="">
                                    <valid>
                                        <add value="+"/>
                                        <add value="-"/>
                                        <add value="|"/>
                                        <add value="."/>
                                        <add value="^"/>
                                        <add value="="/>
                                        <add value="&amp;"/>
                                    </valid>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
        <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
        <data name="fastk_ktab_files" format="fastk_ktab_tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <conditional name="input_type">
                <param name="input_type_selector" value="single"/>
                <param name="input_ktab1" value="fastq1.ktab"/>
                <param name="input_ktab1_tar" value="fastk_in1.tar"/>
                <param name="input_ktab2" value="fastq2.ktab"/>
                <param name="input_ktab2_tar" value="fastk_in2.tar"/>
                <param name="operation_selector" value="and"/>
            </conditional>
            <output name="fastk_hist_out" ftype="fastk_hist">
                <assert_contents>
                    <has_size value="262164"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_out" ftype="fastk_ktab">
                <assert_contents>
                    <has_size value="2064"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
                <assert_contents>
                    <has_archive_member path="logex_ktabs/out.ktab"/>
                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>
                    <has_archive_member path="input_files/input1.ktab"/>
                    <has_archive_member path="input_files/.input1.ktab.1"/>
                    <has_archive_member path="input_files/input2.ktab"/>
                    <has_archive_member path="input_files/.input2.ktab.1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <conditional name="input_type">
                <param name="input_type_selector" value="collection"/>
                <param name="input_ktab_collection">
                    <collection type="list">
                        <element name="input1" value="fastq1.ktab"/>
                        <element name="input2" value="fastq2.ktab"/>
                    </collection>
                </param>
                <param name="input_ktab_collection_tar">
                    <collection type="list">
                        <element name="input1" value="fastk_in1.tar"/>
                        <element name="input2" value="fastk_in2.tar"/>
                    </collection>
                </param>
                <conditional name="operation_sel">
                    <param name="operation_selector_collection" value="and"/>
                </conditional>
            </conditional>
            <output name="fastk_hist_out" ftype="fastk_hist">
                <assert_contents>
                    <has_size value="262164"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_out" ftype="fastk_ktab">
                <assert_contents>
                    <has_size value="2064"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
                <assert_contents>
                    <has_archive_member path="logex_ktabs/out.ktab"/>
                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>
                    <has_archive_member path="input_files/1.ktab"/>
                    <has_archive_member path="input_files/.1.ktab.1"/>
                    <has_archive_member path="input_files/2.ktab"/>
                    <has_archive_member path="input_files/.2.ktab.1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <conditional name="input_type">
                <param name="input_type_selector" value="collection"/>
                <param name="input_ktab_collection">
                    <collection type="list">
                        <element name="input1" value="fastq1.ktab"/>
                        <element name="input2" value="fastq2.ktab"/>
                    </collection>
                </param>
                <param name="input_ktab_collection_tar">
                    <collection type="list">
                        <element name="input1" value="fastk_in1.tar"/>
                        <element name="input2" value="fastk_in2.tar"/>
                    </collection>
                </param>
                <conditional name="operation_sel">
                    <param name="operation_selector_collection" value="unionsum"/>
                </conditional>
            </conditional>
            <output name="fastk_hist_out" ftype="fastk_hist">
                <assert_contents>
                    <has_size value="262164"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_out" ftype="fastk_ktab">
                <assert_contents>
                    <has_size value="2064"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
                <assert_contents>
                    <has_archive_member path="logex_ktabs/out.ktab"/>
                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>
                    <has_archive_member path="input_files/1.ktab"/>
                    <has_archive_member path="input_files/.1.ktab.1"/>
                    <has_archive_member path="input_files/2.ktab"/>
                    <has_archive_member path="input_files/.2.ktab.1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <conditional name="input_type">
                <param name="input_type_selector" value="collection"/>
                <param name="input_ktab_collection">
                    <collection type="list">
                        <element name="input1" value="fastq1.ktab"/>
                        <element name="input2" value="fastq2.ktab"/>
                    </collection>
                </param>
                <param name="input_ktab_collection_tar">
                    <collection type="list">
                        <element name="input1" value="fastk_in1.tar"/>
                        <element name="input2" value="fastk_in2.tar"/>
                    </collection>
                </param>
                <conditional name="operation_sel">
                    <param name="operation_selector_collection" value="custom"/>
                    <param name="custom_expression" value="A&amp;.B"/>
                </conditional>
            </conditional>
            <output name="fastk_hist_out" ftype="fastk_hist">
                <assert_contents>
                    <has_size value="262164"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_out" ftype="fastk_ktab">
                <assert_contents>
                    <has_size value="2064"/>
                </assert_contents>
            </output>
            <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
                <assert_contents>
                    <has_archive_member path="logex_ktabs/out.ktab"/>
                    <has_archive_member path="logex_ktabs/.out.ktab.1"/>
                    <has_archive_member path="input_files/1.ktab"/>
                    <has_archive_member path="input_files/.1.ktab.1"/>
                    <has_archive_member path="input_files/2.ktab"/>
                    <has_archive_member path="input_files/.2.ktab.1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

     Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
     
     The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations.
    
    The tool also supports Ktab file collections as input. The user can select the operation to be performed on the input Ktab files.

    ]]></help>
    <expand macro="citations"/>
</tool>