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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 |
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modified:
macros.xml rg_rnaStarSolo.xml |
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| diff -r 9ee34ba73ebf -r 1cd2511a396e macros.xml --- a/macros.xml Fri Feb 17 20:04:43 2023 +0000 +++ b/macros.xml Wed Feb 22 18:01:29 2023 +0000 |
| [ |
| @@ -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@">1</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"> @@ -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 9ee34ba73ebf -r 1cd2511a396e rg_rnaStarSolo.xml --- a/rg_rnaStarSolo.xml Fri Feb 17 20:04:43 2023 +0000 +++ b/rg_rnaStarSolo.xml Wed Feb 22 18:01:29 2023 +0000 |
| [ |
| b'@@ -122,6 +122,10 @@\n \n --soloOutFormatFeaturesGeneField3 \'${solo.soloOutFormatFeaturesGeneField3}\'\n \n+ ## Unmapped\n+ \'$solo.outSAMunmapped\'\n+ ## Read MAPQ\n+ --outSAMmapqUnique ${solo.outSAMmapqUnique}\n ## Limits\n @LIMITS@\n \n@@ -189,13 +193,13 @@\n <param name="GTFselect" type="select"\n label="Reference genome with annotation"\n help="Select the \'... with builtin gene-model\' option to select from the list of available indexes that were built with splice junction information. Select the \'... without builtin gene-model\' option to select from the list of available indexes without annotated splice junctions, and provide your own splice junction annonations.">\n- <option value="without-gtf" selected=\'true\'>use genome reference without builtin gene-model</option>\n+ <option value="without-gtf-with-gtf" selected=\'true\'>use genome reference without builtin gene-model</option>\n <option value="with-gtf">use genome reference with builtin gene-model</option>\n </param>\n <when value="with-gtf">\n <expand macro="index_selection" with_gene_model="1" />\n </when>\n- <when value="without-gtf">\n+ <when value="without-gtf-with-gtf">\n <expand macro="index_selection" with_gene_model="0" />\n <expand macro="SJDBOPTIONS"/>\n </when>\n@@ -325,7 +329,7 @@\n <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the \'directional\' method given in UMI-tools, Exact collapses only exactly matching UMIs.">\n <expand macro="umidedup_options" />\n <option value="Exact" >Exact</option>\n- <option value="NoDedup" >CellRanger2-4 algorithm</option>\n+ <option value="NoDedup" >Do not deduplicate UMIs</option>\n </param>\n <when value="1MM_All"/>\n <when value="1MM_Directional_UMItools"/>\n@@ -388,12 +392,19 @@\n <expand macro="common_SAM_attributes"/>\n <option value="CR">CR Cellular barcode sequence bases (uncorrected)</option>\n <option value="CY">CY Phred quality of the cellular barcode sequence in the CR tag</option>\n+ <option value="UR">UR UMI (uncorrected)</option>\n+ <option value="UY">UY Phred quality of the UMI</option>\n <option value="GX">GX Gene ID</option>\n <option value="GN">GN Gene name</option>\n <option value="CB">CB Cell identifier (corrected)</option>\n <option value="UB">UB UMI (corrected)</option>\n+ <option value="sM">sM assessment of CB and UMI</option>\n+ <option value="sS">sS sequence of the entire barcode (CB,UMI,adapter...)</option>\n+ <option value="sQ">quality of the entire barcode</option>\n </param>\n <param name="quantModeGene" type="boolean" truevalue="GeneCounts" falsevalue="" checked="false" label="Output global gene count" help="Can be used by MultiQC" />\n+ <param argument="--outSAMunmapped" type="boolean" truevalue="--outSAMunmapped Within" falsevalue="--outSAMunmapped None" checked="false" label="Output unmapped reads in the BAM" />\n+ <expand macro="outSAMmapqUnique"/>\n <expand macro="limits" />\n </section>\n <expand macro="outWig"/>\n@@ -457,7 +468,6 @@\n <data format="txt" name="output_stats" label="${tool.name} on ${on_string}: Barcode/Feature Statistic Summaries"/>\n <data name="reads_per_gene" format="tabular" label="${tool.name} o'..b'utput>\n- <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />\n+ <output name="output_BAM">\n+ <assert_contents>\n+ <has_size value="884669" delta="80000" />\n+ </assert_contents>\n+ </output>\n </test>\n <test expect_num_outputs="6">\n <!-- test 3 -->\n@@ -1153,6 +1169,78 @@\n </assert_contents>\n </output>\n </test>\n+ <test expect_num_outputs="7">\n+ <!-- test 11 indexed -->\n+ <conditional name="refGenomeSource">\n+ <param name="geneSource" value="indexed" />\n+ <conditional name="GTFconditional">\n+ <param name="GTFselect" value="without-gtf-with-gtf" />\n+ <param name="genomeDir" value="000" />\n+ <param name="sjdbOverhang" value="75"/>\n+ <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>\n+ </conditional>\n+ </conditional>\n+ <conditional name="sc" >\n+ <param name="solo_type" value="CB_UMI_Simple" />\n+ <conditional name="input_types">\n+ <param name="use" value="repeat" />\n+ <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />\n+ <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />\n+ </conditional>\n+ <param name="soloCBwhitelist" value="filtered.barcodes.txt" />\n+ <conditional name="params">\n+ <param name="chemistry" value="Cv3" />\n+ </conditional>\n+ <conditional name="umidedup">\n+ <param name="soloUMIdedup" value="1MM_All" />\n+ </conditional>\n+ </conditional>\n+ <section name="solo" >\n+ <conditional name="filter">\n+ <param name="filter_type" value="no_filter" />\n+ </conditional>\n+ <param name="soloStrand" value="Forward" />\n+ <param name="soloFeatures" value="Gene" />\n+ <param name="quantModeGene" value="true" />\n+ </section>\n+ <output name="output_barcodes" >\n+ <assert_contents>\n+ <!-- first and last line -->\n+ <has_line line="AAACCTGAGCGCTCCA" />\n+ <has_line line="TTTGGTTAGTGGGCTA" />\n+ <has_n_lines n="394" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_genes">\n+ <assert_contents>\n+ <has_line_matching expression="GENE1\\s+GENE1\\s+Gene\\s+Expression" />\n+ <has_n_lines n="1" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_matrix" >\n+ <assert_contents>\n+ <has_line_matching expression="1\\s+394\\s+31" />\n+ <has_line_matching expression="1\\s+2\\s+1" />\n+ <has_n_lines n="34" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_stats" >\n+ <assert_contents>\n+ <has_line_matching expression="\\s+noUnmapped\\s+6335" />\n+ <has_line_matching expression="\\s+yesUMIs\\s+33" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_BAM">\n+ <assert_contents>\n+ <has_size value="7133" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ <output name="reads_per_gene" >\n+ <assert_contents>\n+ <has_line_matching expression="GENE1\\s+41\\s+41\\s+0" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n' |