comparison rseqc_macros.xml @ 60:1421603cc95b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d

59:dbedfc5f5a3c

<macros>

    <token name="@TOOL_VERSION@">2.6.4</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.6.4">rseqc</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>

        </stdio>
    </xml>

    <!-- Params -->
    <xml name="bam_param">
        <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
    </xml>

    <xml name="bam_sam_param">
        <param name="input" type="data" label="Input .bam/.sam file" format="bam,sam" help="(--input-file)"/>
    </xml>

    <xml name="refgene_param">
        <param name="refgene" type="data" format="bed12" label="Reference gene model" help="(--refgene)"/>
    </xml>

    <xml name="mapq_param">
        <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot; (--mapq)"/>
    </xml>

    <xml name="readlength_param">
        <param name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/>
    </xml>

    <xml name="readnum_param">
        <param name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/>
    </xml>

    <xml name="sample_size_param">
        <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/>
    </xml>

    <xml name="min_intron_param">
        <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" />
    </xml>

    <xml name="layout_param">
        <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
            <option value="SE" selected="true">Single-end</option>

            <filter>rscript_output</filter>
        </data>
    </xml>

    <!-- Command -->
    <token name="@MULTIHITS@">
<![CDATA[
#if str($multihits_type.multihits_type_selector) == "skip_multihits"
    --skip-multi-hits
    --mapq=${multihits_type.mapq}
#end if
]]>
    </token>

    <token name="@ABOUT@">

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60:1421603cc95b

<macros>
    <token name="@TOOL_VERSION@">5.0.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@GALAXY_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>

        </stdio>
    </xml>

    <!-- Params -->
    <xml name="bam_param">
        <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/>
    </xml>

    <xml name="bam_sam_param">
        <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/>
    </xml>

    <xml name="refgene_param">
        <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
    </xml>

    <xml name="mapq_param">
        <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" 
            help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
    </xml>

    <xml name="readlength_param">
        <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/>
    </xml>

    <xml name="readnum_param">
        <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/>
    </xml>

    <xml name="sample_size_param">
        <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/>
    </xml>

    <xml name="min_intron_param">
        <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" />
    </xml>

    <xml name="layout_param">
        <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
            <option value="SE" selected="true">Single-end</option>

            <filter>rscript_output</filter>
        </data>
    </xml>

    <!-- Command -->
    <token name="@MULTIHITS@"><![CDATA[
        #if str($multihits_type.multihits_type_selector) == "skip_multihits"
            --skip-multi-hits
            --mapq=${multihits_type.mapq}
        #end if
    ]]></token>

    <token name="@BAM_SAM_INPUTS@"><![CDATA[
        #set $extension = str($input.ext)
        ln -s -f '${input}' 'input.${extension}' &&
        #if $extension == 'bam'
            ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
        #end if
    ]]></token>

    <token name="@ABOUT@">

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