comparison macros.xml @ 5:e2d1b5e1eb11 draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6

4:384b972e43bc

<macros>

    <token name="@VERSION_STRING@">1.2</token>

    <token name="@single_or_paired_cmd@">
        #if str( $library.type ) == "single":
            F1=${library.input_1}
        #elif str( $library.type ) == "paired":

            BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
        #end if
    </token>
    <xml name="demultiplexer_common_output_options">
        <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
            truealue="true"
            falsevalue="false"
            checked="true"
        />
        <section name="adv_options" title="Advanced Options" expanded="False">
            <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"

        <param name="RCHAR" type="text"
            label="Replace white space in the read name/header with speficied symbols (RCHAR)"
            help="Set to empty or null for no replacement."
            value=":"/>

        <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
            help="will result in fastq.gz files."
            truevalue="true"
            falsevalue="false"
            checked="false"/>
    </xml>

    <token name="@demultiplexer_common_outputs_cmd@">
        METRICS_FILE_NAME=$METRICS_FILE_NAME
    </token>

        </data>
        <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
            <filter>(adv_options['DIAG'] == 'true')</filter>
        </data>
    </xml>

</macros>

5:e2d1b5e1eb11

<macros>

    <token name="@VERSION_STRING@">1.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.2">je-suite</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>je version 2&gt;&amp;1 | tail -n 1</version_command>
    </xml>

    <token name="@single_or_paired_cmd@">
        #if str( $library.type ) == "single":
            F1=${library.input_1}
        #elif str( $library.type ) == "paired":

            BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
        #end if
    </token>
    <xml name="demultiplexer_common_output_options">
        <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
            truevalue="true"
            falsevalue="false"
            checked="true"
        />
        <section name="adv_options" title="Advanced Options" expanded="False">
            <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"

        <param name="RCHAR" type="text"
            label="Replace white space in the read name/header with speficied symbols (RCHAR)"
            help="Set to empty or null for no replacement."
            value=":"/>

        <param name="GZ" type="hidden" label="Compress output (GZ)"
            help="will result in fastq.gz files."
            value="false"/>
    </xml>

    <token name="@demultiplexer_common_outputs_cmd@">
        METRICS_FILE_NAME=$METRICS_FILE_NAME
    </token>

        </data>
        <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
            <filter>(adv_options['DIAG'] == 'true')</filter>
        </data>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s12859-016-1284-2</citation>
        </citations>
    </xml>
</macros>