| Previous changeset 10:a225487bf618 (2023-02-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54 |
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modified:
data_manager/macros.xml data_manager_conf.xml |
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| diff -r a225487bf618 -r d63c1442407f data_manager/macros.xml --- a/data_manager/macros.xml Fri Feb 17 20:00:58 2023 +0000 +++ b/data_manager/macros.xml Sun Apr 16 08:31:33 2023 +0000 |
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| @@ -5,7 +5,7 @@ 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="@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 @@ -64,23 +64,26 @@ </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> + <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': @@ -219,7 +222,7 @@ </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_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> @@ -231,12 +234,12 @@ </xml> <xml name="cb_match_wl_common"> <option value="Exact" >Exact</option> - <option value="1MM" >Single match</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)</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> + <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." > @@ -278,6 +281,7 @@ <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"> @@ -305,7 +309,7 @@ <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="--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> @@ -397,4 +401,13 @@ <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> |
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| diff -r a225487bf618 -r d63c1442407f data_manager_conf.xml --- a/data_manager_conf.xml Fri Feb 17 20:00:58 2023 +0000 +++ b/data_manager_conf.xml Sun Apr 16 08:31:33 2023 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder" version="0.0.7"> + <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder"> <data_table name="rnastar_index2x_versioned"> <output> <column name="value" /> |