comparison macros.xml @ 13:0e60e2dd20af draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

12:9bd1568619cd

        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.13</token>
    <token name="@PROFILE@">20.05</token>
    <token name="@FLAGS@"><![CDATA[
        #set $flags = 0
        #if $filter
            #set $flags = sum(map(int, str($filter).split(',')))
        #end if

        #else
            #set use_ref=False
        #end if
    ]]></token>

    <xml name="optional_reference">
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Use a reference sequence">
                <help>@HELP@</help>
                <option value="no">No</option>
                <option value="history">Use a genome/index from the history</option>

        </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>

13:0e60e2dd20af

        <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@">1.20</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">22.05</token>
    <token name="@FLAGS@"><![CDATA[
        #set $flags = 0
        #if $filter
            #set $flags = sum(map(int, str($filter).split(',')))
        #end if

        #else
            #set use_ref=False
        #end if
    ]]></token>

    <xml name="optional_reference" token_help="" token_argument="">
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Use a reference sequence">
                <help>@HELP@</help>
                <option value="no">No</option>
                <option value="history">Use a genome/index from the history</option>

        </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>