comparison macros.xml @ 8:a53efedba9e7 draft

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

7:10184eaa85fc

        <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
            #end if
        #end for
    ]]></token>
    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
        ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
        ##and sets the -t/-T parameters accordingly:
        ##- in case of history a symbolic link is used because samtools (view) will generate
        ##  the index which might not be possible in the directory containing the fasta file
        ##- in case of cached the absolute path is used which allows to read the cram file
        ##  without specifying the reference
        #if $addref_cond.addref_select == "history":
            ln -s '${addref_cond.ref}' reference.fa &&
            samtools faidx reference.fa &&
            #set reffa="reference.fa"
            #set reffai="reference.fa.fai"
        #elif $addref_cond.addref_select == "cached":
            #set reffa=str($addref_cond.ref.fields.path)
            #set reffai=str($addref_cond.ref.fields.path)+".fai"
        #else
            #set reffa=None
            #set reffai=None
        #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>

8:a53efedba9e7

        <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(',')))

                #end if
            #end if
        #end for
    ]]></token>
    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
        ## Make the user-selected reference genome, if any, accessible through
        ## a shell variable $reffa, index the reference if necessary, and make
        ## the fai-index file available through a shell variable $reffai.

        ## For a cached genome simply sets the shell variables to point to the
        ## genome file and its precalculated index.
        ## For a genome from the user's history, if that genome is a plain
        ## fasta file, the code creates a symlink in the pwd, creates the fai
        ## index file next to it, then sets the shell variables to point to the
        ## symlink and its index.
        ## For a fasta.gz dataset from the user's history, it tries the same,
        ## but this will only succeed if the file got compressed with bgzip.
        ## For a regular gzipped file samtools faidx will fail, in which case
        ## the code falls back to decompressing to plain fasta before
        ## reattempting the indexing.
        ## Indexing of a bgzipped file produces a regular fai index file *and*
        ## a compressed gzi file. The former is identical to the fai index of
        ## the uncompressed fasta.

        ## If the user has not selected a reference (it's an optional parameter
        ## in some samtools wrappers), a cheetah boolean use_ref is set to
        ## False to encode that fact.

        #set use_ref=True
        #if $addref_cond.addref_select == "history":
            #if $addref_cond.ref.is_of_type('fasta'):
                reffa="reference.fa" &&
                ln -s '${addref_cond.ref}' \$reffa &&
                samtools faidx \$reffa &&
            #else:
                reffa="reference.fa.gz" &&
                ln -s '${addref_cond.ref}' \$reffa &&
                {
                    samtools faidx \$reffa ||
                    {
                        echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
                        gzip -dc \$reffa > reference.fa &&
                        reffa="reference.fa" &&
                        samtools faidx \$reffa;
                    }
                } &&
            #end if
            reffai=\$reffa.fai &&
        #elif $addref_cond.addref_select == "cached":
            ## in case of cached the absolute path is used which allows to read 
            ## a cram file  without specifying the reference
            reffa='${addref_cond.ref.fields.path}' &&
            reffai=\$reffa.fai &&
        #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>