comparison macros.xml @ 8:a389f74c3630 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit cd62639660bef041ba14ecff337fb98e84e75d8a

7:ce32171c6d44

        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.15.1</token>
    <token name="@PROFILE@">20.05</token>
    <token name="@FLAGS@"><![CDATA[
        #set $flags = 0
        #if $filter
            #set $flags = sum(map(int, str($filter).split(',')))

        </conditional>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/},}
            </citation>
            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
            <citation type="bibtex">
                @misc{Danecek_et_al,
                Author={Danecek, P., Schiffels, S., Durbin, R.},
                title={Multiallelic calling model in bcftools (-m)},
                url = {http://samtools.github.io/bcftools/call-m.pdf},}
            </citation>
            <citation type="bibtex">
                @misc{Durbin_VCQC,
                Author={Durbin, R.},
                title={Segregation based metric for variant call QC},
                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
            </citation>
            <citation type="bibtex">
                @misc{Li_SamMath,
                Author={Li, H.},
                title={Mathematical Notes on SAMtools Algorithms},
                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
            </citation>
            <citation type="bibtex">
                @misc{SamTools_github,
                title={SAMTools GitHub page},
                url = {https://github.com/samtools/samtools},}
            </citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
    </xml>

8:a389f74c3630

        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <!-- NOTE: for some tools only the version of the requirement but not the
        tool's version is controlled by the TOOL_VERSION token 
        (because their version is ahead of the requirement version .. 
         please only bump the minor version in order to let the requirement
         version catch up eventually). To find the tools check:
        `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
    <token name="@TOOL_VERSION@">1.15.1</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">20.05</token>
    <token name="@FLAGS@"><![CDATA[
        #set $flags = 0
        #if $filter
            #set $flags = sum(map(int, str($filter).split(',')))

        </conditional>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/gigascience/giab008</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
    </xml>