comparison macros.xml @ 2:457b09031d57 draft

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1:82aac94b06c3

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.22">bedtools</requirement>
            <yield/>
        </requirements>
        <version_command>bedtools --version</version_command>
    </xml>
    <token name="@WRAPPER_VERSION@">2.22</token>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->

            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>
    <xml name="reciprocal">
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require that the fraction of overlap be reciprocal for A and B"
            help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" />

            </when>
            <when value="False" />
        </conditional>
    </xml>
    <xml name="split">
        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" 
            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 
            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
    </xml>
    <xml name="genome">
        <param format="tabular" name="genome" type="data" label="Genome file" />
        <!--TODO: make use of: ${chromInfo} -->

    </xml>

    <!-- ToDo column_picker -->
    <xml name="choose_columns">
        <param name="cols" type="text" value=""
            label="Specify the column(s) (comma separated) that should be summarized"
            help="(-c)">
            <sanitizer invalid_char="">
                <valid initial="string.digits"><add value=","/></valid>
            </sanitizer>
        </param>
    </xml>

    <xml name="choose_operations">
        <param name="operation" type="select" label="Specify the operation">
            <yield />
        </param>

2:457b09031d57

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.22">bedtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">2.22</token>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->

            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
        <version_command>bedtools --version</version_command>
    </xml>
    <xml name="reciprocal">
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require that the fraction of overlap be reciprocal for A and B"
            help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" />

            </when>
            <when value="False" />
        </conditional>
    </xml>
    <xml name="split">
        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
    </xml>
    <xml name="genome">
        <param format="tabular" name="genome" type="data" label="Genome file" />
        <!--TODO: make use of: ${chromInfo} -->

    </xml>

    <!-- ToDo column_picker -->
    <xml name="choose_columns">
        <param name="cols" type="text" value=""
            label="Specify the column(s) that should be summarized"
            help="comma separated (-c)">
            <sanitizer invalid_char="">
                <valid initial="string.digits"><add value=","/></valid>
            </sanitizer>
        </param>
    </xml>

    <xml name="choose_column">
        <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
    </xml>

    <token name="@C_AND_O_ARGUMENT@">
        #set $col = list()
        #set $op = list()
        #for $item in $c_and_o_argument_repeat:
            #silent $col.append( str($item.col) )
            #silent $op.append( str($item.operation) )
        #end for
        #if $col:
            -c #echo ','.join($col)#
            -o #echo ','.join($op)#
        #end if
    </token>

    <xml name="c_and_o_argument">
        <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
            <expand macro="choose_column" />
            <expand macro="choose_operations">
                <expand macro="math_options" />
                <expand macro="additional_math_options" />
            </expand>
        </repeat>
    </xml>


    <xml name="choose_operations">
        <param name="operation" type="select" label="Specify the operation">
            <yield />
        </param>