comparison data_manager/macros.xml @ 11:d63c1442407f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54

10:a225487bf618

    whenever you make changes to the @TOOL_VERSION@ token!
    The data manager uses a symlink to this macro file to keep the STAR and
    the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
    <!-- STAR version to be used -->
    <token name="@TOOL_VERSION@">2.7.10b</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:

         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
    </xml>
    <xml name="dbKeyActions">
        <actions>
            <conditional name="refGenomeSource.geneSource">
                <when value="indexed">
                    <action type="metadata" name="dbkey">
                        <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
                            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                            <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
                        </option>
                    </action>
                </when>
                <when value="history">
                    <action type="metadata" name="dbkey">
                        <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
                    </action>
                </when>
            </conditional>
        </actions>
    </xml>
    <token name="@TEMPINDEX@"><![CDATA[
    ## Create temporary index for custom reference
    #if str($refGenomeSource.geneSource) == 'history':
        #if $refGenomeSource.genomeFastaFiles.ext == "fasta"

                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
            </when>
        </conditional>
    </xml>
    <xml name="umidedup_options">
        <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option>
        <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
        <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
    </xml>
    <xml name="anchor_types">
        <option value="0">Read start</option>

        <option value="2">Adapter start</option>
        <option value="3">Adapter end</option>
    </xml>
    <xml name="cb_match_wl_common">
        <option value="Exact" >Exact</option>
        <option value="1MM" >Single match</option>
    </xml>
    <xml name="cb_match_wl_cellranger">
        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option>
    </xml>
    <xml name="solo_adapter_params">
        <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
            <sanitizer>
                <valid initial="string.digits">

        </section>
    </xml>
    <xml name="outCountActions">
        <actions>
            <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
        </actions>
    </xml>
    <xml name="outWig">
        <conditional name="outWig">
            <param name="outWigType" type="select" label="Compute coverage">

        <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
            <option value="">Default (everything that mapped)</option>
            <option value="read_5p">signal from only 5’ of the 1st read</option>
            <option value="read2">signal from only 2nd read</option>
        </param>
        <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="collapse strands (unstranded coverage)" help="By default, the strands are separated."/>
        <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
        <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
    </xml>
    <token name="@OUTWIG@"><![CDATA[
        #if str($outWig.outWigType) != 'None':

                <option value="-">No per gene or transcript output as no GTF was provided</option>
            </param>
            <when value="-" />
        </conditional>
    </xml>
</macros>

11:d63c1442407f

    whenever you make changes to the @TOOL_VERSION@ token!
    The data manager uses a symlink to this macro file to keep the STAR and
    the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
    <!-- STAR version to be used -->
    <token name="@TOOL_VERSION@">2.7.10b</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@PROFILE@">21.01</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:

         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
    </xml>
    <xml name="dbKeyActions">
        <actions>
            <expand macro="dbKeyAction"/>
        </actions>
    </xml>
    <xml name="dbKeyAction">
        <conditional name="refGenomeSource.geneSource">
            <when value="indexed">
                <action type="metadata" name="dbkey">
                    <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                        <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
                    </option>
                </action>
            </when>
            <when value="history">
                <action type="metadata" name="dbkey">
                    <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
                </action>
            </when>
        </conditional>
    </xml>
    <token name="@TEMPINDEX@"><![CDATA[
    ## Create temporary index for custom reference
    #if str($refGenomeSource.geneSource) == 'history':
        #if $refGenomeSource.genomeFastaFiles.ext == "fasta"

                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
            </when>
        </conditional>
    </xml>
    <xml name="umidedup_options">
        <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
        <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
        <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
    </xml>
    <xml name="anchor_types">
        <option value="0">Read start</option>

        <option value="2">Adapter start</option>
        <option value="3">Adapter end</option>
    </xml>
    <xml name="cb_match_wl_common">
        <option value="Exact" >Exact</option>
        <option value="1MM" >Single match (1MM)</option>
    </xml>
    <xml name="cb_match_wl_cellranger">
        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option>
        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
    </xml>
    <xml name="solo_adapter_params">
        <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
            <sanitizer>
                <valid initial="string.digits">

        </section>
    </xml>
    <xml name="outCountActions">
        <actions>
            <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
            <expand macro="dbKeyAction"/>
        </actions>
    </xml>
    <xml name="outWig">
        <conditional name="outWig">
            <param name="outWigType" type="select" label="Compute coverage">

        <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
            <option value="">Default (everything that mapped)</option>
            <option value="read_5p">signal from only 5’ of the 1st read</option>
            <option value="read2">signal from only 2nd read</option>
        </param>
        <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/>
        <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
        <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
    </xml>
    <token name="@OUTWIG@"><![CDATA[
        #if str($outWig.outWigType) != 'None':

                <option value="-">No per gene or transcript output as no GTF was provided</option>
            </param>
            <when value="-" />
        </conditional>
    </xml>
    <xml name="outSAMmapqUnique">
        <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
        - according to SAM/BAM specs it means "undefined".
        - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
        <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
        label="MAPQ value for unique mappers"
        help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
    </xml>
</macros>