annotate GATK/gatk/print_reads.xml @ 2:2c7824a8d764 draft

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<macros>
    <xml name="PrintReadsParameters" tokens="tag">
        
        <expand macro="macro_bam_input" tag="@TAG@" />

        <!-- BQSR in main config -->

        <expand macro="macro_optional_parameters">

            <param name="number" type="integer" value="" optional="true" label="Print the first n reads from the file, discarding the rest" help="-n,&#8209;&#8209;number &amp;lt;number&amp;gt;" />

            <param name="platform" type="text" value="" optional="true" label="Exclude all reads with this platform from the output" help="-platform,&#8209;&#8209;platform &amp;lt;platform&amp;gt;" />

            <param name="readGroup" type="text" value="" optional="true" label="Exclude all reads with this read group from the output" help="-readGroup,&#8209;&#8209;readGroup &amp;lt;readGroup&amp;gt;" />

            <param name="sample_file" type="data" format="txt" optional="true" label="File containing a list of samples (one per line). Can be specified multiple times" help="-sf,&#8209;&#8209;sample_file &amp;lt;sample_file&amp;gt;" />

            <repeat name="sample_names" title="Sample names to be included in the analysis" help="-sn,‑‑sample_name &amp;lt;sample_name&amp;gt;">
                <param name="sample_name" type="text" value="" title="Sample name to be included in the analysis" />
            </repeat>
            
            <param name="simplify" type="text" truevalue="-s" falsevalue="" label="Erase all extra attributes in the read but keep the read group information" help="-s,&#8209;&#8209;simplify" />

        </expand>

    </xml>

    <xml name="PrintReadsOutput">
        <data format="bam" name="pr_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)">
            <yield />
        </data>
    </xml>

    <template name="PrintReadsPreprocessing">
<![CDATA[
        @token_bam_input_pre@
]]>
    </template>

    <template name="PrintReadsOptions">
<![CDATA[
        --out                   ${pr_output_bam}

        @token_bam_input@

        #set $optionals = $analysis_type.optional_parameters
        #if $optionals.optional_parameters_enabled
            #if int($optionals.number) > 0
                --number $optionals.number
            #end if
            #if str($optionals.platform)
                --platform $optionals.platform
            #end if
            #if str($optionals.readGroup)
                --readGroup $optionals.readGroup
            #end if
            #if $optionals.sample_file
                --sample_file $optionals.sample_file
            #end if
            #if $optionals.sample_names
                #for $sample in $optionals.sample_names:
                    --intervals ${sample.sample_name}
                #end for
            #end if
            $optionals.simplify
        #end if
]]>
    </template>
</macros>