comparison macros.xml @ 3:b91e0f76afe9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit b3426aed6615742d96dfb8f7346a9e0d4e391a99-dirty

2:02afb5ea2fce

        ##- 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=str($addref_cond.ref)
            #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)
        #else
            #set reffa=None
            #set reffai=None
        #end if
    ]]></token>
    <token name="@ADDTHREADS@"><![CDATA[
        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
    ]]></token>

    <token name="@ADDMEMORY@"><![CDATA[
        ##compute the number of memory available to samtools sort (-m)
        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
        ((addmemory=addmemory*75/100)) &&

        <option value="256">alignment or read is not primary</option>
        <option value="512">read fails platform/vendor quality checks</option>
        <option value="1024">read is a PCR or optical duplicate</option>
        <option value="2048">supplementary alignment</option>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},

3:b91e0f76afe9

        ##- 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>
    <token name="@ADDTHREADS@"><![CDATA[
        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
    ]]></token>
    <token name="@ADDMEMORY@"><![CDATA[
        ##compute the number of memory available to samtools sort (-m)
        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
        ((addmemory=addmemory*75/100)) &&

        <option value="256">alignment or read is not primary</option>
        <option value="512">read fails platform/vendor quality checks</option>
        <option value="1024">read is a PCR or optical duplicate</option>
        <option value="2048">supplementary alignment</option>
    </xml>

    <!-- region specification macros and tokens for tools that allow the specification 
         of region by bed file / space separated list of regions -->
    <token name="@REGIONS_FILE@"><![CDATA[
        #if $cond_region.select_region == 'tab':
            -t '$cond_region.targetregions'
        #end if
    ]]></token>
    <token name="@REGIONS_MANUAL@"><![CDATA[
        #if $cond_region.select_region == 'text':
            #for $i, $x in enumerate($cond_region.regions_repeat):
               '${x.region}'
            #end for
        #end if
    ]]></token>
    <xml name="regions_macro">
        <conditional name="cond_region">
            <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
                <option value="no" selected="True">No</option>
                <option value="text">Manualy specify regions</option>
                <option value="tab">Regions from tabular file</option>
            </param>
            <when value="no"/>
            <when value="text">
                <repeat name="regions_repeat" min="1" default="1" title="Regions">
                    <param name="region" type="text" label="region" help="format chr:from-to">
                        <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
                    </param>
                </repeat>
            </when>
            <when value="tab">
                <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
            </when>
        </conditional>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},